rs11618172

Variant names:

• chr13-37612353-T-C
• rs11618172

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 0.294 in 152,084 control chromosomes in the GnomAD database, including 7,012 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 0.29 (7012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

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 (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.294 AC: 44699 AN: 151964 Hom.: 7002 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44726 AN: 152084 Hom.: 7012 Cov.: 32 AF XY: 0.285 AC XY: 21215 AN XY: 74340

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.313

Alfa AF: 0.322 Hom.: 1398

Bravo AF: 0.295

Asia WGS AF: 0.257 AC: 894 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	1.2
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11618172; hg19: chr13-38186490;