7-48755540-C-T

Variant names:

• chr7-48755540-C-T
• rs2363125

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 0.423 in 152,084 control chromosomes in the GnomAD database, including 13,898 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 0.42 (13898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.423 AC: 64255 AN: 151966 Hom.: 13899 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.423 AC: 64272 AN: 152084 Hom.: 13898 Cov.: 32 AF XY: 0.429 AC XY: 31857 AN XY: 74322

African (AFR) AF: 0.351 AC: 14548 AN: 41470

American (AMR) AF: 0.420 AC: 6430 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3061 AN: 5170

South Asian (SAS) AF: 0.463 AC: 2228 AN: 4816

European-Finnish (FIN) AF: 0.479 AC: 5071 AN: 10580

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30115 AN: 67974

Other (OTH) AF: 0.426 AC: 897 AN: 2108

Alfa AF: 0.436 Hom.: 9932

Bravo AF: 0.413

Asia WGS AF: 0.470 AC: 1635 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	1.1
DANN	Benign	0.55
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs2363125; hg19: chr7-48795136;