chr2-203930071-C-A

Variant names:

• chr2-203930071-C-A
• rs4294983

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 0.152 in 152,004 control chromosomes in the GnomAD database, including 2,903 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 0.15 (2903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 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: 0.152 AC: 23073 AN: 151886 Hom.: 2891 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.152 AC: 23126 AN: 152004 Hom.: 2903 Cov.: 32 AF XY: 0.153 AC XY: 11350 AN XY: 74290

African (AFR) AF: 0.329 AC: 13636 AN: 41408

American (AMR) AF: 0.115 AC: 1761 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1484 AN: 5156

South Asian (SAS) AF: 0.125 AC: 602 AN: 4822

European-Finnish (FIN) AF: 0.0470 AC: 496 AN: 10562

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4203 AN: 68004

Other (OTH) AF: 0.141 AC: 297 AN: 2100

Alfa AF: 0.0850 Hom.: 670

Bravo AF: 0.167

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4294983; hg19: chr2-204794794;