11-57481648-G-A

Variant names:

• chr11-57481648-G-A
• rs2955849

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 0.417 in 143,064 control chromosomes in the GnomAD database, including 12,897 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 0.42 (12897 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 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: 0.417 AC: 59640 AN: 142974 Hom.: 12901 Cov.: 23

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.417 AC: 59650 AN: 143064 Hom.: 12897 Cov.: 23 AF XY: 0.427 AC XY: 29521 AN XY: 69086

African (AFR) AF: 0.318 AC: 12031 AN: 37842

American (AMR) AF: 0.452 AC: 6252 AN: 13846

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1674 AN: 3414

East Asian (EAS) AF: 0.678 AC: 3255 AN: 4802

South Asian (SAS) AF: 0.529 AC: 2335 AN: 4414

European-Finnish (FIN) AF: 0.518 AC: 4795 AN: 9248

Middle Eastern (MID) AF: 0.481 AC: 130 AN: 270

European-Non Finnish (NFE) AF: 0.420 AC: 27869 AN: 66402

Other (OTH) AF: 0.430 AC: 835 AN: 1942

Alfa AF: 0.412 Hom.: 28315

Bravo AF: 0.401

Asia WGS AF: 0.519 AC: 1771 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0040
DANN	Benign	0.49
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs2955849; hg19: chr11-57249121;