2-41853484-T-G

Variant names:

• chr2-41853484-T-G
• rs4305317

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 0.474 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.474 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

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.472

Alfa AF: 0.463 Hom.: 32559

Bravo AF: 0.471

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4305317; hg19: chr2-42080624;