1-102737551-T-C

Variant names:

• chr1-102737551-T-C
• rs1376359

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.608 in 151,498 control chromosomes in the GnomAD database, including 30,799 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 0.61 (30799 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.666
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92141 AN: 151380 Hom.: 30794 Cov.: 29

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.622

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.608 AC: 92171 AN: 151498 Hom.: 30799 Cov.: 29 AF XY: 0.615 AC XY: 45520 AN XY: 73996

African (AFR) AF: 0.308 AC: 12738 AN: 41302

American (AMR) AF: 0.701 AC: 10639 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2084 AN: 3462

East Asian (EAS) AF: 0.615 AC: 3136 AN: 5098

South Asian (SAS) AF: 0.643 AC: 3088 AN: 4806

European-Finnish (FIN) AF: 0.817 AC: 8593 AN: 10520

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49756 AN: 67832

Other (OTH) AF: 0.624 AC: 1313 AN: 2104

Alfa AF: 0.677 Hom.: 76160

Bravo AF: 0.590

Asia WGS AF: 0.623 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1376359; hg19: chr1-103203107;