rs11040270

Positions:

• chr11-49144118-G-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 0.14 in 151,922 control chromosomes in the GnomAD database, including 1,935 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 0.14 (1935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 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: 0.140 AC: 21298 AN: 151804 Hom.: 1928 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.140 AC: 21338 AN: 151922 Hom.: 1935 Cov.: 32 AF XY: 0.140 AC XY: 10428 AN XY: 74266

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0692

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.125

Alfa AF: 0.117 Hom.: 178

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11040270; hg19: chr11-49165670;