rs3754734

Positions:

• chr2-27076730-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;