7-51762547-T-C

Variant names:

• chr7-51762547-T-C
• rs637056

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 0.538 in 152,126 control chromosomes in the GnomAD database, including 22,838 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 0.54 (22838 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.538 AC: 81816 AN: 152008 Hom.: 22811 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.538 AC: 81895 AN: 152126 Hom.: 22838 Cov.: 33 AF XY: 0.534 AC XY: 39688 AN XY: 74386

African (AFR) AF: 0.686 AC: 28439 AN: 41486

American (AMR) AF: 0.451 AC: 6890 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2182 AN: 3472

East Asian (EAS) AF: 0.552 AC: 2857 AN: 5174

South Asian (SAS) AF: 0.486 AC: 2345 AN: 4822

European-Finnish (FIN) AF: 0.434 AC: 4596 AN: 10582

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32872 AN: 67980

Other (OTH) AF: 0.551 AC: 1164 AN: 2114

Alfa AF: 0.499 Hom.: 3085

Bravo AF: 0.551

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs637056; hg19: chr7-51830243;