chr7-63886508-C-T

Variant names:

• chr7-63886508-C-T
• rs13437751

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;