chr7-131630333-G-A

Position:

• chr7-131630333-G-A

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 0.477 in 152,098 control chromosomes in the GnomAD database, including 21,639 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 0.48 (21639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.477 AC: 72514 AN: 151980 Hom.: 21643 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.477 AC: 72495 AN: 152098 Hom.: 21639 Cov.: 32 AF XY: 0.470 AC XY: 34954 AN XY: 74346

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.507

Alfa AF: 0.639 Hom.: 61336

Bravo AF: 0.457

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.43
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs929731; hg19: chr7-131315092;