rs11662635

chr18-57503042-G-A

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 0.0555 in 152,250 control chromosomes in the GnomAD database, including 769 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 0.055 (769 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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 (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.0553 AC: 8418 AN: 152130 Hom.: 759 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0555 AC: 8447 AN: 152250 Hom.: 769 Cov.: 33 AF XY: 0.0618 AC XY: 4598 AN XY: 74442

Gnomad4 AFR AF: 0.0121

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0564

Alfa AF: 0.0344 Hom.: 116

Bravo AF: 0.0687

Asia WGS AF: 0.151 AC: 523 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	2.1
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11662635; hg19: chr18-55170274;