7-131772384-T-A

Variant names:

• chr7-131772384-T-A
• rs7787173

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 0.831 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.740 AC: 30704 AN: 41514

American (AMR) AF: 0.879 AC: 13451 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4711 AN: 5184

South Asian (SAS) AF: 0.692 AC: 3336 AN: 4824

European-Finnish (FIN) AF: 0.908 AC: 9626 AN: 10598

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58604 AN: 68022

Other (OTH) AF: 0.835 AC: 1759 AN: 2106

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs7787173; hg19: chr7-131457143;