rs11875674

Variant names:

• chr18-56467257-T-C
• rs11875674

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 0.183 in 152,176 control chromosomes in the GnomAD database, including 2,962 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 0.18 (2962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.183 AC: 27841 AN: 152058 Hom.: 2958 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.183 AC: 27837 AN: 152176 Hom.: 2962 Cov.: 32 AF XY: 0.186 AC XY: 13815 AN XY: 74394

African (AFR) AF: 0.0724 AC: 3006 AN: 41542

American (AMR) AF: 0.181 AC: 2772 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3468

East Asian (EAS) AF: 0.137 AC: 707 AN: 5172

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4824

European-Finnish (FIN) AF: 0.258 AC: 2734 AN: 10582

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16082 AN: 67990

Other (OTH) AF: 0.210 AC: 444 AN: 2110

Alfa AF: 0.221 Hom.: 2033

Bravo AF: 0.172

Asia WGS AF: 0.198 AC: 690 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11875674; hg19: chr18-54134488;