11-55482003-G-A

Variant names:

• chr11-55482003-G-A
• rs649358

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 0.422 in 151,678 control chromosomes in the GnomAD database, including 14,955 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 (14955 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 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: 0.423 AC: 64053 AN: 151560 Hom.: 14940 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.422 AC: 64078 AN: 151678 Hom.: 14955 Cov.: 31 AF XY: 0.426 AC XY: 31568 AN XY: 74084

African (AFR) AF: 0.219 AC: 9065 AN: 41380

American (AMR) AF: 0.553 AC: 8400 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1949 AN: 3464

East Asian (EAS) AF: 0.522 AC: 2664 AN: 5100

South Asian (SAS) AF: 0.444 AC: 2135 AN: 4806

European-Finnish (FIN) AF: 0.525 AC: 5538 AN: 10540

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32739 AN: 67878

Other (OTH) AF: 0.448 AC: 945 AN: 2110

Alfa AF: 0.434 Hom.: 1975

Bravo AF: 0.420

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs649358; hg19: chr11-55249479;