1-48507138-C-T

Variant names:

• chr1-48507138-C-T
• rs1343124

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 0.642 in 152,040 control chromosomes in the GnomAD database, including 33,869 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 0.64 (33869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.76 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: 0.642 AC: 97562 AN: 151922 Hom.: 33856 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.642 AC: 97605 AN: 152040 Hom.: 33869 Cov.: 32 AF XY: 0.642 AC XY: 47741 AN XY: 74326

African (AFR) AF: 0.354 AC: 14678 AN: 41428

American (AMR) AF: 0.757 AC: 11566 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2810 AN: 3470

East Asian (EAS) AF: 0.689 AC: 3553 AN: 5160

South Asian (SAS) AF: 0.635 AC: 3057 AN: 4814

European-Finnish (FIN) AF: 0.714 AC: 7546 AN: 10572

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52043 AN: 67990

Other (OTH) AF: 0.664 AC: 1403 AN: 2114

Alfa AF: 0.731 Hom.: 169426

Bravo AF: 0.635

Asia WGS AF: 0.652 AC: 2267 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	2.8
DANN	Benign	0.69
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1343124; hg19: chr1-48972810; COSMIC: COSV59942719;