1-152469813-T-C

Variant names:

• chr1-152469813-T-C
• rs6661961

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 0.582 in 151,948 control chromosomes in the GnomAD database, including 25,676 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 0.58 (25676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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: 0.581 AC: 88285 AN: 151830 Hom.: 25645 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.582 AC: 88364 AN: 151948 Hom.: 25676 Cov.: 32 AF XY: 0.584 AC XY: 43387 AN XY: 74284

African (AFR) AF: 0.581 AC: 24048 AN: 41426

American (AMR) AF: 0.577 AC: 8806 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1766 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3199 AN: 5172

South Asian (SAS) AF: 0.508 AC: 2451 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6900 AN: 10524

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39183 AN: 67950

Other (OTH) AF: 0.592 AC: 1249 AN: 2110

Alfa AF: 0.574 Hom.: 41972

Bravo AF: 0.575

Asia WGS AF: 0.565 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.74
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6661961; hg19: chr1-152442289;