rs10486661

Variant names:

• chr7-35271245-T-A
• rs10486661

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 0.138 in 152,274 control chromosomes in the GnomAD database, including 1,617 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 0.14 (1617 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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: 0.138 AC: 20966 AN: 152156 Hom.: 1616 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.138 AC: 20975 AN: 152274 Hom.: 1617 Cov.: 33 AF XY: 0.133 AC XY: 9927 AN XY: 74474

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.182

Alfa AF: 0.143 Hom.: 222

Bravo AF: 0.142

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486661; hg19: chr7-35310856;