rs11010897

Positions:

• chr10-36818775-G-A
• chr10-36818775-G-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 0.486 in 150,572 control chromosomes in the GnomAD database, including 18,216 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 0.49 (18216 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.486 AC: 73153 AN: 150454 Hom.: 18199 Cov.: 27

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.486 AC: 73195 AN: 150572 Hom.: 18216 Cov.: 27 AF XY: 0.490 AC XY: 36004 AN XY: 73420

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.478

Alfa AF: 0.332 Hom.: 855

Bravo AF: 0.491

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11010897; hg19: chr10-37107703;