7-131999774-T-A

Position:

• chr7-131999774-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.868 in 152,218 control chromosomes in the GnomAD database, including 57,637 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 0.87 (57637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.868 AC: 132074 AN: 152100 Hom.: 57573 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.868 AC: 132201 AN: 152218 Hom.: 57637 Cov.: 32 AF XY: 0.870 AC XY: 64710 AN XY: 74402

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.854

Alfa AF: 0.854 Hom.: 6904

Bravo AF: 0.873

Asia WGS AF: 0.939 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6467410; hg19: chr7-131684533;