rs13437751

chr7-63886508-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.199 in 152,024 control chromosomes in the GnomAD database, including 4,442 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 0.20 (4442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30222 AN: 151908 Hom.: 4413 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.199 AC: 30302 AN: 152024 Hom.: 4442 Cov.: 32 AF XY: 0.201 AC XY: 14921 AN XY: 74316

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.178

Alfa AF: 0.142 Hom.: 1028

Bravo AF: 0.216

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.5
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13437751; hg19: chr7-63346886;