rs2098910

Variant names:

• chr18-74533367-G-C
• rs2098910

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;