rs649358

chr11-55482003-G-Achr11-55482003-G-Cchr11-55482003-G-T

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 0.422 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.448

Alfa AF: 0.443 Hom.: 1953

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs649358; hg19: chr11-55249479;