rs10227696

Variant names:

• chr7-116521893-G-A
• rs10227696

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 0.167 in 152,122 control chromosomes in the GnomAD database, including 2,290 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 0.17 (2290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 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: 0.167 AC: 25336 AN: 152004 Hom.: 2294 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.167 AC: 25334 AN: 152122 Hom.: 2290 Cov.: 32 AF XY: 0.161 AC XY: 11967 AN XY: 74380

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.179

Alfa AF: 0.177 Hom.: 608

Bravo AF: 0.174

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10227696; hg19: chr7-116161947;