1-248317466-C-T

Variant names:

• chr1-248317466-C-T
• rs4309013

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 0.786 in 152,080 control chromosomes in the GnomAD database, including 47,280 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 0.79 (47280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 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: 0.786 AC: 119374 AN: 151962 Hom.: 47242 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.786 AC: 119466 AN: 152080 Hom.: 47280 Cov.: 32 AF XY: 0.790 AC XY: 58724 AN XY: 74314

African (AFR) AF: 0.848 AC: 35187 AN: 41496

American (AMR) AF: 0.784 AC: 11984 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2429 AN: 3464

East Asian (EAS) AF: 0.860 AC: 4430 AN: 5150

South Asian (SAS) AF: 0.874 AC: 4201 AN: 4808

European-Finnish (FIN) AF: 0.802 AC: 8485 AN: 10574

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50144 AN: 67978

Other (OTH) AF: 0.764 AC: 1613 AN: 2110

Alfa AF: 0.743 Hom.: 18469

Bravo AF: 0.785

Asia WGS AF: 0.858 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs4309013; hg19: chr1-248480768;