11-49241473-A-C

Variant names:

• chr11-49241473-A-C
• rs11040295

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0111 in 145,132 control chromosomes in the GnomAD database, including 60 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 0.011 (60 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0111 (1614/145132) while in subpopulation EAS AF = 0.0372 (188/5050). AF 95% confidence interval is 0.0329. There are 60 homozygotes in GnomAd4. There are 757 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 60 gene

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: 0.0111 AC: 1611 AN: 145120 Hom.: 60 Cov.: 28

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00323

Gnomad ASJ AF: 0.000583

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.00403

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000844

Gnomad OTH AF: 0.0102

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

GnomAD4 genome AF: 0.0111 AC: 1614 AN: 145132 Hom.: 60 Cov.: 28 AF XY: 0.0107 AC XY: 757 AN XY: 70504

African (AFR) AF: 0.0324 AC: 1283 AN: 39558

American (AMR) AF: 0.00323 AC: 46 AN: 14234

Ashkenazi Jewish (ASJ) AF: 0.000583 AC: 2 AN: 3430

East Asian (EAS) AF: 0.0372 AC: 188 AN: 5050

South Asian (SAS) AF: 0.00405 AC: 19 AN: 4696

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8676

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 278

European-Non Finnish (NFE) AF: 0.000844 AC: 56 AN: 66328

Other (OTH) AF: 0.0101 AC: 20 AN: 1976

Alfa AF: 0.00940 Hom.: 4

Bravo AF: 0.0129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.38
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11040295; hg19: chr11-49263025;