7-51367982-A-T

Variant names:

• chr7-51367982-A-T
• rs573461

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 0.32 in 152,246 control chromosomes in the GnomAD database, including 8,234 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 0.32 (8234 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.319 AC: 48591 AN: 152128 Hom.: 8218 Cov.: 34

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.320 AC: 48662 AN: 152246 Hom.: 8234 Cov.: 34 AF XY: 0.317 AC XY: 23572 AN XY: 74416

African (AFR) AF: 0.371 AC: 15397 AN: 41556

American (AMR) AF: 0.410 AC: 6273 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2779 AN: 5166

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4828

European-Finnish (FIN) AF: 0.238 AC: 2520 AN: 10598

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18800 AN: 68014

Other (OTH) AF: 0.316 AC: 667 AN: 2110

Alfa AF: 0.307 Hom.: 911

Bravo AF: 0.341

Asia WGS AF: 0.368 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.81
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs573461; hg19: chr7-51435679; COSMIC: COSV107154847;