rs7899151

chr10-81189166-G-Achr10-81189166-G-T

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 0.747 in 151,366 control chromosomes in the GnomAD database, including 42,393 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 0.75 (42393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.747 AC: 112993 AN: 151248 Hom.: 42371 Cov.: 30

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.747 AC: 113064 AN: 151366 Hom.: 42393 Cov.: 30 AF XY: 0.745 AC XY: 55103 AN XY: 73956

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.791

Alfa AF: 0.736 Hom.: 4851

Bravo AF: 0.753

Asia WGS AF: 0.783 AC: 2721 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.2
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7899151; hg19: chr10-82948922;