2-41794811-A-T

Variant names:

• chr2-41794811-A-T
• rs4558632

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.457 AC: 18901 AN: 41404

American (AMR) AF: 0.281 AC: 4293 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.181 AC: 934 AN: 5164

South Asian (SAS) AF: 0.252 AC: 1219 AN: 4828

European-Finnish (FIN) AF: 0.257 AC: 2713 AN: 10576

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20714 AN: 67946

Other (OTH) AF: 0.295 AC: 623 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.83
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4558632; hg19: chr2-42021951;