dbSNP rs4447485: ENSG00000267737:n.532C>T (chr17-78342606-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000823933.1(ENSG00000267737):n.532C>T 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 0.149 in 152,424 control chromosomes in the GnomAD database, including 1,802 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 0.15 ( 1800 hom., cov: 32)

Exomes 𝑓: 0.13 ( 2 hom. )

Consequence

ENSG00000267737
ENST00000823933.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.390

Publications

7 publications found

Variant links:

Genes affected

ENSG00000267737 (HGNC:):

ENSG00000267737 links:

Genome browser will be placed here

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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188633.1 link	n.540C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105371912	NR_188632.1 link	n.74-1359C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000267737	ENST00000823933.1 link	n.532C>T	non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000267737	ENST00000586321.1 link	n.61-1359C>T	intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1 link	n.39-1359C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22691

AN:

152064

Hom.:

1802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.324

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.0929

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.128

AC:

AN:

242

Hom.:

AF XY:

0.139

AC XY:

AN XY:

180

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.200

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.137

AC:

AN:

182

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.149

AC:

22688

AN:

152182

Hom.:

1800

Cov.:

AF XY:

0.148

AC XY:

11044

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.132

AC:

5479

AN:

41522

American (AMR)

AF:

0.126

AC:

1931

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

882

AN:

3472

East Asian (EAS)

AF:

0.0929

AC:

479

AN:

5156

South Asian (SAS)

AF:

0.150

AC:

723

AN:

4830

European-Finnish (FIN)

AF:

0.135

AC:

1436

AN:

10608

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.162

AC:

11043

AN:

67974

Other (OTH)

AF:

0.169

AC:

358

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1003

2006

3010

4013

5016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.161

Hom.:

3280

Bravo

AF:

0.148

Asia WGS

AF:

0.120

AC:

418

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

6.1

(source)

DANN

Benign

0.88

PhyloP100

0.39

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