rs11875173

Variant names:

• chr18-67188712-T-C
• rs11875173

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 0.227 in 152,036 control chromosomes in the GnomAD database, including 4,806 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 0.23 (4806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 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: 0.227 AC: 34489 AN: 151920 Hom.: 4813 Cov.: 32

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.227 AC: 34478 AN: 152036 Hom.: 4806 Cov.: 32 AF XY: 0.224 AC XY: 16639 AN XY: 74306

African (AFR) AF: 0.0753 AC: 3126 AN: 41504

American (AMR) AF: 0.241 AC: 3679 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3468

East Asian (EAS) AF: 0.171 AC: 883 AN: 5150

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4808

European-Finnish (FIN) AF: 0.192 AC: 2031 AN: 10564

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.308 AC: 20936 AN: 67948

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.292 Hom.: 8862

Bravo AF: 0.223

Asia WGS AF: 0.255 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.85
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11875173; hg19: chr18-64855949;