1-119426994-C-T

Variant names:

• chr1-119426994-C-T
• rs947129

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 0.691 in 151,996 control chromosomes in the GnomAD database, including 36,372 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 0.69 (36372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.691 AC: 104974 AN: 151878 Hom.: 36344 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.691 AC: 105052 AN: 151996 Hom.: 36372 Cov.: 32 AF XY: 0.694 AC XY: 51548 AN XY: 74290

African (AFR) AF: 0.728 AC: 30197 AN: 41462

American (AMR) AF: 0.727 AC: 11100 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3601 AN: 5170

South Asian (SAS) AF: 0.638 AC: 3061 AN: 4800

European-Finnish (FIN) AF: 0.706 AC: 7459 AN: 10564

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45080 AN: 67946

Other (OTH) AF: 0.674 AC: 1420 AN: 2108

Alfa AF: 0.696 Hom.: 6034

Bravo AF: 0.696

Asia WGS AF: 0.663 AC: 2307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.40
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs947129; hg19: chr1-119969617; COSMIC: COSV65592870;