2-4172909-T-C

Variant names:

• chr2-4172909-T-C
• rs4850057

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 0.177 in 146,662 control chromosomes in the GnomAD database, including 4,572 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 0.18 (4572 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.177 AC: 25875 AN: 146542 Hom.: 4572 Cov.: 29

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0967

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.177 AC: 25889 AN: 146662 Hom.: 4572 Cov.: 29 AF XY: 0.175 AC XY: 12500 AN XY: 71398

African (AFR) AF: 0.147 AC: 6034 AN: 41124

American (AMR) AF: 0.124 AC: 1796 AN: 14538

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 246 AN: 3266

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5176

South Asian (SAS) AF: 0.196 AC: 917 AN: 4678

European-Finnish (FIN) AF: 0.225 AC: 2189 AN: 9712

Middle Eastern (MID) AF: 0.0971 AC: 27 AN: 278

European-Non Finnish (NFE) AF: 0.220 AC: 14270 AN: 65006

Other (OTH) AF: 0.148 AC: 300 AN: 2024

Alfa AF: 0.207 Hom.: 3489

Asia WGS AF: 0.0920 AC: 318 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.6
DANN	Benign	0.39
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4850057; hg19: chr2-4220499;