1-248317466-C-T

Variant names:

• chr1-248317466-C-T
• rs4309013

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.764

Alfa AF: 0.743 Hom.: 16330

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4309013; hg19: chr1-248480768;