rs10500736

chr11-10985161-T-C

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 0.328 in 151,886 control chromosomes in the GnomAD database, including 8,524 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 0.33 (8524 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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: 0.328 AC: 49713 AN: 151768 Hom.: 8511 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.328 AC: 49759 AN: 151886 Hom.: 8524 Cov.: 31 AF XY: 0.325 AC XY: 24153 AN XY: 74212

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.320

Alfa AF: 0.311 Hom.: 2297

Bravo AF: 0.334

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500736; hg19: chr11-11006708;