rs11036431

chr11-5244450-G-A

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 0.299 in 151,746 control chromosomes in the GnomAD database, including 7,027 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 0.30 (7023 hom., cov: 31)
  • Exomes 𝑓: 0.29 (4 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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: 0.299 AC: 45282 AN: 151586 Hom.: 7008 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.286 AC: 12 AN: 42 Hom.: 4 AF XY: 0.263 AC XY: 10 AN XY: 38

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.299 AC: 45334 AN: 151704 Hom.: 7023 Cov.: 31 AF XY: 0.293 AC XY: 21754 AN XY: 74126

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.297

Alfa AF: 0.313 Hom.: 942

Bravo AF: 0.304

Asia WGS AF: 0.316 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.1
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11036431; hg19: chr11-5265680; COSMIC: COSV57964243;