rs2421930

Variant names:

• chr2-117443528-C-G
• rs2421930

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 0.0999 in 152,206 control chromosomes in the GnomAD database, including 1,412 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 0.10 (1412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.0996 AC: 15153 AN: 152088 Hom.: 1395 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0999 AC: 15199 AN: 152206 Hom.: 1412 Cov.: 32 AF XY: 0.0997 AC XY: 7422 AN XY: 74420

African (AFR) AF: 0.241 AC: 10011 AN: 41502

American (AMR) AF: 0.0970 AC: 1484 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.00888 AC: 46 AN: 5178

South Asian (SAS) AF: 0.123 AC: 594 AN: 4826

European-Finnish (FIN) AF: 0.0414 AC: 439 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0330 AC: 2244 AN: 68010

Other (OTH) AF: 0.0806 AC: 170 AN: 2108

Alfa AF: 0.0770 Hom.: 107

Bravo AF: 0.108

Asia WGS AF: 0.0810 AC: 283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.71
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs2421930; hg19: chr2-118201104;