rs2124349

chr18-67349863-G-Achr18-67349863-G-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 0.0665 in 152,114 control chromosomes in the GnomAD database, including 395 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 0.067 (395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0644 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: 0.0665 AC: 10112 AN: 151996 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0543

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0540

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0665 AC: 10121 AN: 152114 Hom.: 395 Cov.: 32 AF XY: 0.0697 AC XY: 5181 AN XY: 74328

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0660

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0644 Hom.: 721

Bravo AF: 0.0601

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2124349; hg19: chr18-65017100;