7-53588976-T-C

Variant names:

• chr7-53588976-T-C
• rs10245298

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 0.881 in 152,240 control chromosomes in the GnomAD database, including 59,102 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 0.88 (59102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.881 AC: 133961 AN: 152122 Hom.: 59054 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.881 AC: 134067 AN: 152240 Hom.: 59102 Cov.: 32 AF XY: 0.884 AC XY: 65810 AN XY: 74432

African (AFR) AF: 0.875 AC: 36341 AN: 41544

American (AMR) AF: 0.899 AC: 13749 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4762 AN: 5168

South Asian (SAS) AF: 0.893 AC: 4315 AN: 4832

European-Finnish (FIN) AF: 0.913 AC: 9680 AN: 10602

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59447 AN: 68022

Other (OTH) AF: 0.879 AC: 1854 AN: 2110

Alfa AF: 0.877 Hom.: 18433

Bravo AF: 0.877

Asia WGS AF: 0.884 AC: 3076 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	1.2
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10245298; hg19: chr7-53656669;