rs2098910

Positions:

• chr18-74533367-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 0.722 in 152,130 control chromosomes in the GnomAD database, including 40,360 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 0.72 (40360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109778 AN: 152012 Hom.: 40358 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.722 AC: 109813 AN: 152130 Hom.: 40360 Cov.: 32 AF XY: 0.726 AC XY: 53988 AN XY: 74366

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.753

Alfa AF: 0.735 Hom.: 3858

Bravo AF: 0.719

Asia WGS AF: 0.806 AC: 2798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2098910; hg19: chr18-72200602;