1-62359119-T-C

Variant names:

• chr1-62359119-T-C
• rs3861941

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 0.347 in 152,224 control chromosomes in the GnomAD database, including 10,832 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 0.35 (10832 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52798 AN: 152106 Hom.: 10804 Cov.: 33

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.347 AC: 52885 AN: 152224 Hom.: 10832 Cov.: 33 AF XY: 0.345 AC XY: 25650 AN XY: 74446

African (AFR) AF: 0.565 AC: 23445 AN: 41510

American (AMR) AF: 0.370 AC: 5659 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1555 AN: 5178

South Asian (SAS) AF: 0.361 AC: 1742 AN: 4830

European-Finnish (FIN) AF: 0.191 AC: 2028 AN: 10608

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16497 AN: 68016

Other (OTH) AF: 0.343 AC: 725 AN: 2112

Alfa AF: 0.289 Hom.: 24050

Bravo AF: 0.371

Asia WGS AF: 0.303 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.43
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs3861941; hg19: chr1-62824790;