rs3098610

Variant names:

• chr2-231853332-T-C
• rs3098610

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.924 AC: 38241 AN: 41392

American (AMR) AF: 0.595 AC: 9057 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2544 AN: 3470

East Asian (EAS) AF: 0.130 AC: 666 AN: 5138

South Asian (SAS) AF: 0.560 AC: 2686 AN: 4794

European-Finnish (FIN) AF: 0.722 AC: 7578 AN: 10500

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48403 AN: 67928

Other (OTH) AF: 0.682 AC: 1434 AN: 2102

Alfa AF: 0.707 Hom.: 59352

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs3098610; hg19: chr2-232718042;