rs11873377

chr18-74495461-T-Cchr18-74495461-T-G

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 0.109 in 152,152 control chromosomes in the GnomAD database, including 1,558 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 0.11 (1558 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 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: 0.109 AC: 16601 AN: 152034 Hom.: 1557 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.109 AC: 16611 AN: 152152 Hom.: 1558 Cov.: 33 AF XY: 0.107 AC XY: 7989 AN XY: 74394

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.0478

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0748

Gnomad4 FIN AF: 0.0552

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.0309 Hom.: 27

Bravo AF: 0.116

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11873377; hg19: chr18-72162696;