rs4312490

Variant names:

• chr2-240882064-T-C
• rs4312490

Your query was ambiguous. Multiple possible variants found:

• chr2-240882064-T-C
• chr2-240882064-T-G

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 0.585 in 152,040 control chromosomes in the GnomAD database, including 26,377 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 0.59 (26377 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.585 AC: 88927 AN: 151922 Hom.: 26347 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.585 AC: 88994 AN: 152040 Hom.: 26377 Cov.: 33 AF XY: 0.581 AC XY: 43189 AN XY: 74324

African (AFR) AF: 0.581 AC: 24074 AN: 41462

American (AMR) AF: 0.516 AC: 7895 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3046 AN: 5174

South Asian (SAS) AF: 0.396 AC: 1906 AN: 4816

European-Finnish (FIN) AF: 0.676 AC: 7145 AN: 10562

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41230 AN: 67958

Other (OTH) AF: 0.573 AC: 1210 AN: 2112

Alfa AF: 0.534 Hom.: 3299

Bravo AF: 0.577

Asia WGS AF: 0.492 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4312490; hg19: chr2-241821481;