2-41853484-T-G

Variant names:

• chr2-41853484-T-G
• rs4305317

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 0.474 in 152,070 control chromosomes in the GnomAD database, including 17,161 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 0.47 (17161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.564 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: 0.474 AC: 71989 AN: 151952 Hom.: 17151 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.474 AC: 72028 AN: 152070 Hom.: 17161 Cov.: 33 AF XY: 0.473 AC XY: 35187 AN XY: 74332

African (AFR) AF: 0.510 AC: 21157 AN: 41464

American (AMR) AF: 0.385 AC: 5883 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3468

East Asian (EAS) AF: 0.581 AC: 3012 AN: 5182

South Asian (SAS) AF: 0.535 AC: 2579 AN: 4824

European-Finnish (FIN) AF: 0.439 AC: 4640 AN: 10564

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31573 AN: 67990

Other (OTH) AF: 0.472 AC: 994 AN: 2104

Alfa AF: 0.467 Hom.: 74242

Bravo AF: 0.471

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.75
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs4305317; hg19: chr2-42080624;