2-41829412-G-T

Variant names:

• chr2-41829412-G-T
• rs726548

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 0.465 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.464 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

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.422

Alfa AF: 0.290 Hom.: 675

Bravo AF: 0.482

Asia WGS AF: 0.368 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726548; hg19: chr2-42056552;