dbSNP rs10485170: ENSG00000279565:n.673T>C (chr6-88172933-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000624253.1(ENSG00000279565):n.673T>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 0.141 in 152,220 control chromosomes in the GnomAD database, including 2,011 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 0.14 ( 2011 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000279565
ENST00000624253.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.202

Publications

19 publications found

Variant links:

Genes affected

ENSG00000279565 (HGNC:):

ENSG00000279565 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=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000279565	ENST00000624253.1 link	n.673T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298549	ENST00000756364.1 link	n.129-38664T>C	intron_variant	Intron 1 of 2
ENSG00000298549	ENST00000756365.1 link	n.571+2664T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21468

AN:

152102

Hom.:

2009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.0923

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.0808

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0990

Gnomad OTH

AF:

0.121

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)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.141

AC:

21485

AN:

152220

Hom.:

2011

Cov.:

AF XY:

0.138

AC XY:

10311

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.268

AC:

11113

AN:

41492

American (AMR)

AF:

0.0921

AC:

1409

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

413

AN:

3470

East Asian (EAS)

AF:

0.00251

AC:

AN:

5188

South Asian (SAS)

AF:

0.0800

AC:

386

AN:

4822

European-Finnish (FIN)

AF:

0.104

AC:

1105

AN:

10618

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0990

AC:

6735

AN:

68010

Other (OTH)

AF:

0.120

AC:

253

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

871

1741

2612

3482

4353

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.112

Hom.:

3659

Bravo

AF:

0.146

Asia WGS

AF:

0.0650

AC:

230

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

4.4

(source)

DANN

Benign

0.63

PhyloP100

0.20

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