rs2724509

Positions:

• chr3-27683361-G-A
• chr3-27683361-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 0.132 in 152,122 control chromosomes in the GnomAD database, including 1,563 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 0.13 (1563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20142 AN: 152004 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.132 AC: 20145 AN: 152122 Hom.: 1563 Cov.: 32 AF XY: 0.129 AC XY: 9600 AN XY: 74356

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.0605

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.161

Alfa AF: 0.169 Hom.: 4912

Bravo AF: 0.129

Asia WGS AF: 0.0420 AC: 145 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
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: rs2724509; hg19: chr3-27724852;