chr11-49144118-G-C

Variant names:

• chr11-49144118-G-C
• rs11040270

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.244 AC: 10125 AN: 41428

American (AMR) AF: 0.122 AC: 1862 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3468

East Asian (EAS) AF: 0.167 AC: 859 AN: 5148

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4820

European-Finnish (FIN) AF: 0.0695 AC: 734 AN: 10566

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0902 AC: 6124 AN: 67912

Other (OTH) AF: 0.125 AC: 263 AN: 2112

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
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs11040270; hg19: chr11-49165670;