rs7850481

chr9-108032463-G-Achr9-108032463-G-C

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 0.401 in 151,918 control chromosomes in the GnomAD database, including 13,399 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 0.40 (13399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 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: 0.401 AC: 60812 AN: 151800 Hom.: 13387 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.401 AC: 60855 AN: 151918 Hom.: 13399 Cov.: 32 AF XY: 0.413 AC XY: 30636 AN XY: 74244

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.430

Alfa AF: 0.384 Hom.: 1419

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	9.0
Dann	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7850481; hg19: chr9-110794744;