dbSNP rs16918797: SUGT1P4-STRA6LP:n.2674G>C (chr9-97296793-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000375204.3(SUGT1P4-STRA6LP):n.2674G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0375 in 152,270 control chromosomes in the GnomAD database, including 327 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.037 ( 327 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SUGT1P4-STRA6LP
ENST00000375204.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.757

Publications

0 publications found

Variant links:

Genes affected

SUGT1P4-STRA6LP (HGNC:53834): (SUGT1P4-STRA6LP readthrough) This locus is a fusion of a partial duplication of SUGT1 at the 5' end and the ortholog of mouse 1300002K09Rik (GeneID:74152) at the 3' end. A frameshift disrupts the potential open reading frame, so this locus is considered to be a transcribed pseudogene in humans. In addition, read-through transcripts extending into the downstream locus (GeneID:100499483) are observed. [provided by RefSeq, Aug 2010]

SUGT1P4-STRA6LP links:

SUGT1P4-STRA6LP-CCDC180 (HGNC:53835): (SUGT1P4-STRA6LP-CCDC180 readthrough) This locus represents a set of read-through transcripts spanning an upstream pseudogene (GeneID:100499484) extending into a downstream protein-coding locus (GeneID:100499483). All of the read-through transcripts are candidates for nonsense-mediated decay (NMD), so they are not thought to express a protein. [provided by RefSeq, Aug 2010]

SUGT1P4-STRA6LP-CCDC180 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SUGT1P4-STRA6LP	NR_036526.1 link	n.2697G>C	non_coding_transcript_exon_variant	Exon 16 of 16
SUGT1P4-STRA6LP-CCDC180	NR_036527.1 link	n.1403+1802G>C	intron_variant	Intron 14 of 48
SUGT1P4-STRA6LP-CCDC180	NR_036528.1 link	n.1403+1802G>C	intron_variant	Intron 14 of 50
SUGT1P4-STRA6LP-CCDC180	NR_036529.1 link	n.1092+5306G>C	intron_variant	Intron 12 of 44

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SUGT1P4-STRA6LP	ENST00000375204.3 link	n.2674G>C	non_coding_transcript_exon_variant	Exon 16 of 16	2
SUGT1P4-STRA6LP	ENST00000800023.1 link	n.1897G>C	non_coding_transcript_exon_variant	Exon 15 of 15
SUGT1P4-STRA6LP-CCDC180	ENST00000375206.6 link	n.1332+1802G>C	intron_variant	Intron 14 of 48	2

Frequencies

GnomAD3 genomes

AF:

0.0375

AC:

5708

AN:

152152

Hom.:

329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0177

Gnomad ASJ

AF:

0.0340

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00253

Gnomad OTH

AF:

0.0411

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

AF:

0.0375

AC:

5710

AN:

152270

Hom.:

327

Cov.:

AF XY:

0.0356

AC XY:

2654

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.121

AC:

5037

AN:

41500

American (AMR)

AF:

0.0177

AC:

271

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0340

AC:

118

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.00166

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.000188

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00253

AC:

172

AN:

68032

Other (OTH)

AF:

0.0407

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

259

518

776

1035

1294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0250

Hom.:

Bravo

AF:

0.0438

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.1

(source)

DANN

Benign

0.77

PhyloP100

0.76

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over