rs11152236

Variant names:

• chr18-60553938-T-C
• rs11152236

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 0.432 in 151,992 control chromosomes in the GnomAD database, including 14,892 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 0.43 (14892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.433 AC: 65721 AN: 151874 Hom.: 14892 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.432 AC: 65733 AN: 151992 Hom.: 14892 Cov.: 33 AF XY: 0.443 AC XY: 32948 AN XY: 74302

African (AFR) AF: 0.328 AC: 13577 AN: 41420

American (AMR) AF: 0.518 AC: 7909 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3733 AN: 5168

South Asian (SAS) AF: 0.630 AC: 3037 AN: 4822

European-Finnish (FIN) AF: 0.505 AC: 5334 AN: 10566

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29305 AN: 67972

Other (OTH) AF: 0.431 AC: 907 AN: 2104

Alfa AF: 0.441 Hom.: 7885

Bravo AF: 0.427

Asia WGS AF: 0.647 AC: 2246 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.86
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs11152236; hg19: chr18-58221171; COSMIC: COSV72769321;