rs11253857

Positions:

• chr10-6658154-A-G

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 0.145 in 152,206 control chromosomes in the GnomAD database, including 1,935 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 0.15 (1935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

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 (SAS) allele frequency at 95% confidence interval = 0.25 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: 0.145 AC: 22102 AN: 152088 Hom.: 1935 Cov.: 32

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.145 AC: 22100 AN: 152206 Hom.: 1935 Cov.: 32 AF XY: 0.147 AC XY: 10936 AN XY: 74404

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.150

Alfa AF: 0.175 Hom.: 3306

Bravo AF: 0.138

Asia WGS AF: 0.230 AC: 799 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	1.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11253857; hg19: chr10-6700116;