rs7850212

Positions:

• chr9-134307318-C-A
• chr9-134307318-C-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 0.112 in 152,176 control chromosomes in the GnomAD database, including 1,178 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 0.11 (1178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 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: 0.112 AC: 17021 AN: 152052 Hom.: 1178 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.112 AC: 17023 AN: 152176 Hom.: 1178 Cov.: 32 AF XY: 0.107 AC XY: 7988 AN XY: 74406

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0386

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0905

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0646 Hom.: 86

Bravo AF: 0.120

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7850212; hg19: chr9-137199164;