rs11201253

Positions:

• chr10-84829146-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 0.0627 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0593

Alfa AF: 0.0207 Hom.: 54

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11201253; hg19: chr10-86588902;