1-68392796-A-G

Variant names:

• chr1-68392796-A-G
• rs3125923

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 0.263 in 152,028 control chromosomes in the GnomAD database, including 6,572 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 0.26 (6572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.263 AC: 39974 AN: 151910 Hom.: 6555 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.263 AC: 40038 AN: 152028 Hom.: 6572 Cov.: 32 AF XY: 0.266 AC XY: 19759 AN XY: 74332

African (AFR) AF: 0.447 AC: 18529 AN: 41416

American (AMR) AF: 0.245 AC: 3737 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2383 AN: 5164

South Asian (SAS) AF: 0.354 AC: 1697 AN: 4800

European-Finnish (FIN) AF: 0.134 AC: 1424 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11157 AN: 67984

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.190 Hom.: 5466

Bravo AF: 0.278

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs3125923; hg19: chr1-68858479;