rs11256534

chr10-10215050-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 0.0563 in 152,194 control chromosomes in the GnomAD database, including 336 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 0.056 (336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0808 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: 0.0563 AC: 8568 AN: 152076 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0563 AC: 8563 AN: 152194 Hom.: 336 Cov.: 32 AF XY: 0.0561 AC XY: 4173 AN XY: 74388

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.0304

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.0755

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.0461

Alfa AF: 0.0750 Hom.: 247

Bravo AF: 0.0522

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.22
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11256534; hg19: chr10-10257013;