7-131772384-T-A

Position:

• chr7-131772384-T-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 0.831 in 152,230 control chromosomes in the GnomAD database, including 52,927 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 0.83 (52927 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126409 AN: 152112 Hom.: 52890 Cov.: 34

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.831 AC: 126498 AN: 152230 Hom.: 52927 Cov.: 34 AF XY: 0.831 AC XY: 61847 AN XY: 74446

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.835

Alfa AF: 0.833 Hom.: 2738

Bravo AF: 0.829

Asia WGS AF: 0.799 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7787173; hg19: chr7-131457143;