2-3865230-T-C

Variant names:

• chr2-3865230-T-C
• rs4849999

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 0.914 in 152,240 control chromosomes in the GnomAD database, including 63,649 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 0.91 (63649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.923 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: 0.914 AC: 139058 AN: 152122 Hom.: 63597 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.914 AC: 139170 AN: 152240 Hom.: 63649 Cov.: 32 AF XY: 0.912 AC XY: 67911 AN XY: 74434

African (AFR) AF: 0.897 AC: 37277 AN: 41544

American (AMR) AF: 0.936 AC: 14316 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3202 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4294 AN: 5162

South Asian (SAS) AF: 0.829 AC: 3992 AN: 4814

European-Finnish (FIN) AF: 0.937 AC: 9942 AN: 10608

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63200 AN: 68024

Other (OTH) AF: 0.918 AC: 1942 AN: 2116

Alfa AF: 0.923 Hom.: 103659

Bravo AF: 0.916

Asia WGS AF: 0.836 AC: 2907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4849999; hg19: chr2-3912820;