1-102668353-A-G

Variant names:

• chr1-102668353-A-G
• rs10874639

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 0.112 in 152,092 control chromosomes in the GnomAD database, including 1,119 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 0.11 (1119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17059 AN: 151974 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.112 AC: 17075 AN: 152092 Hom.: 1119 Cov.: 32 AF XY: 0.111 AC XY: 8244 AN XY: 74340

African (AFR) AF: 0.0761 AC: 3163 AN: 41556

American (AMR) AF: 0.118 AC: 1796 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1536 AN: 5178

South Asian (SAS) AF: 0.112 AC: 538 AN: 4822

European-Finnish (FIN) AF: 0.0738 AC: 783 AN: 10610

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.126 AC: 8561 AN: 67874

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.109 Hom.: 1909

Bravo AF: 0.116

Asia WGS AF: 0.202 AC: 697 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.68
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs10874639; hg19: chr1-103133909; COSMIC: COSV59980784;