rs11875173

Positions:

• chr18-67188712-T-C

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 0.227 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0753

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.269

Alfa AF: 0.303 Hom.: 7257

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11875173; hg19: chr18-64855949;