rs3098610

Variant names:

• chr2-231853332-T-C
• rs3098610

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 0.735 in 151,756 control chromosomes in the GnomAD database, including 43,031 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 0.73 (43031 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

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 = 0.916 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: 0.735 AC: 111399 AN: 151638 Hom.: 42977 Cov.: 29

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.735 AC: 111497 AN: 151756 Hom.: 43031 Cov.: 29 AF XY: 0.725 AC XY: 53761 AN XY: 74148

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.682

Alfa AF: 0.700 Hom.: 44998

Bravo AF: 0.733

Asia WGS AF: 0.360 AC: 1257 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	1.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3098610; hg19: chr2-232718042;