1-242691129-T-C

Variant names:

• chr1-242691129-T-C
• rs6692131

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 0.753 in 152,156 control chromosomes in the GnomAD database, including 43,390 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 0.75 (43390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114553 AN: 152038 Hom.: 43368 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.753 AC: 114619 AN: 152156 Hom.: 43390 Cov.: 32 AF XY: 0.751 AC XY: 55843 AN XY: 74378

African (AFR) AF: 0.785 AC: 32600 AN: 41514

American (AMR) AF: 0.651 AC: 9954 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2671 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4291 AN: 5164

South Asian (SAS) AF: 0.771 AC: 3710 AN: 4812

European-Finnish (FIN) AF: 0.703 AC: 7444 AN: 10588

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51294 AN: 68004

Other (OTH) AF: 0.767 AC: 1618 AN: 2110

Alfa AF: 0.728 Hom.: 6849

Bravo AF: 0.751

Asia WGS AF: 0.758 AC: 2638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6692131; hg19: chr1-242854431;