rs11201253

Variant names:

• chr10-84829146-C-T
• rs11201253

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0627 in 152,238 control chromosomes in the GnomAD database, including 552 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 0.063 (552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 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: 0.0627 AC: 9537 AN: 152120 Hom.: 552 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0627 AC: 9552 AN: 152238 Hom.: 552 Cov.: 32 AF XY: 0.0633 AC XY: 4713 AN XY: 74436

African (AFR) AF: 0.130 AC: 5379 AN: 41528

American (AMR) AF: 0.105 AC: 1605 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3472

East Asian (EAS) AF: 0.144 AC: 747 AN: 5186

South Asian (SAS) AF: 0.126 AC: 605 AN: 4818

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 872 AN: 68022

Other (OTH) AF: 0.0593 AC: 125 AN: 2108

Alfa AF: 0.0330 Hom.: 446

Bravo AF: 0.0723

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11201253; hg19: chr10-86588902;