7-81170518-T-G

Variant names:

• chr7-81170518-T-G
• rs500454

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 0.99 in 152,050 control chromosomes in the GnomAD database, including 74,516 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 0.99 (74516 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 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: 0.990 AC: 150402 AN: 151932 Hom.: 74459 Cov.: 31

Gnomad AFR AF: 0.999

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.990 AC: 150518 AN: 152050 Hom.: 74516 Cov.: 31 AF XY: 0.988 AC XY: 73435 AN XY: 74316

Gnomad4 AFR AF: 0.999

Gnomad4 AMR AF: 0.997

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.992

Alfa AF: 0.987 Hom.: 9352

Bravo AF: 0.994

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500454; hg19: chr7-80799834;