2-41829412-G-T

Variant names:

• chr2-41829412-G-T
• rs726548

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 0.465 in 151,980 control chromosomes in the GnomAD database, including 17,068 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 0.46 (17068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.464 AC: 70516 AN: 151862 Hom.: 17027 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.465 AC: 70613 AN: 151980 Hom.: 17068 Cov.: 32 AF XY: 0.460 AC XY: 34202 AN XY: 74280

African (AFR) AF: 0.589 AC: 24433 AN: 41450

American (AMR) AF: 0.486 AC: 7430 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5156

South Asian (SAS) AF: 0.441 AC: 2118 AN: 4808

European-Finnish (FIN) AF: 0.363 AC: 3839 AN: 10568

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28946 AN: 67934

Other (OTH) AF: 0.422 AC: 893 AN: 2114

Alfa AF: 0.310 Hom.: 824

Bravo AF: 0.482

Asia WGS AF: 0.368 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.45
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs726548; hg19: chr2-42056552;