rs11246602

Variant names:

• chr11-54607190-A-G
• rs11246602

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 0.11 in 151,870 control chromosomes in the GnomAD database, including 1,118 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 0.11 (1118 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 48 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 (EAS) allele frequency at 95% confidence interval = 0.147 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: 0.110 AC: 16714 AN: 151748 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.110 AC: 16706 AN: 151870 Hom.: 1118 Cov.: 32 AF XY: 0.114 AC XY: 8454 AN XY: 74236

African (AFR) AF: 0.0568 AC: 2358 AN: 41526

American (AMR) AF: 0.0978 AC: 1490 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 308 AN: 3464

East Asian (EAS) AF: 0.156 AC: 806 AN: 5178

South Asian (SAS) AF: 0.149 AC: 717 AN: 4816

European-Finnish (FIN) AF: 0.203 AC: 2134 AN: 10522

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.127 AC: 8580 AN: 67818

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.116 Hom.: 1747

Bravo AF: 0.100

Asia WGS AF: 0.124 AC: 428 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs11246602; hg19: chr11-51512090;