rs3754734

Variant names:

• chr2-27076730-G-T
• rs3754734

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 0.525 in 152,076 control chromosomes in the GnomAD database, including 22,629 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 0.53 (22629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.526 AC: 79870 AN: 151958 Hom.: 22622 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.525 AC: 79886 AN: 152076 Hom.: 22629 Cov.: 32 AF XY: 0.528 AC XY: 39271 AN XY: 74366

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.551

Alfa AF: 0.509 Hom.: 3918

Bravo AF: 0.494

Asia WGS AF: 0.680 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754734; hg19: chr2-27299598;