rs10885211

Positions:

• chr10-111564544-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 0.511 in 152,040 control chromosomes in the GnomAD database, including 20,577 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 0.51 (20577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.511 AC: 77635 AN: 151922 Hom.: 20551 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.511 AC: 77693 AN: 152040 Hom.: 20577 Cov.: 32 AF XY: 0.508 AC XY: 37780 AN XY: 74316

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.510

Alfa AF: 0.482 Hom.: 3111

Bravo AF: 0.506

Asia WGS AF: 0.390 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885211; hg19: chr10-113324302;