rs2729313

Variant names:

• chr3-1992671-C-T
• rs2729313

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0851 in 152,022 control chromosomes in the GnomAD database, including 682 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 0.085 (682 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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: 0.0850 AC: 12913 AN: 151904 Hom.: 677 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0851 AC: 12943 AN: 152022 Hom.: 682 Cov.: 32 AF XY: 0.0840 AC XY: 6245 AN XY: 74326

African (AFR) AF: 0.148 AC: 6115 AN: 41436

American (AMR) AF: 0.0424 AC: 648 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0462 AC: 222 AN: 4808

European-Finnish (FIN) AF: 0.0677 AC: 715 AN: 10564

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0720 AC: 4898 AN: 67982

Other (OTH) AF: 0.0720 AC: 152 AN: 2110

Alfa AF: 0.0914 Hom.: 168

Bravo AF: 0.0853

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	12
DANN	Benign	0.53
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2729313; hg19: chr3-2034355;