2-41794811-A-T

Variant names:

• chr2-41794811-A-T
• rs4558632

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.333 in 151,980 control chromosomes in the GnomAD database, including 9,011 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 0.33 (9011 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.333 AC: 50611 AN: 151860 Hom.: 8980 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.333 AC: 50675 AN: 151980 Hom.: 9011 Cov.: 31 AF XY: 0.329 AC XY: 24473 AN XY: 74316

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.295

Alfa AF: 0.159 Hom.: 285

Bravo AF: 0.343

Asia WGS AF: 0.252 AC: 882 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4558632; hg19: chr2-42021951;