chr2-4172909-T-C

Variant names:

• chr2-4172909-T-C
• rs4850057

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.177 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

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.148

Alfa AF: 0.207 Hom.: 3244

Asia WGS AF: 0.0920 AC: 318 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4850057; hg19: chr2-4220499;