rs2089739

Positions:

• chr3-162160925-C-A

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 0.657 in 152,064 control chromosomes in the GnomAD database, including 35,667 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 0.66 (35667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 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: 0.658 AC: 99936 AN: 151946 Hom.: 35653 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.657 AC: 99978 AN: 152064 Hom.: 35667 Cov.: 32 AF XY: 0.654 AC XY: 48649 AN XY: 74330

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.685

Alfa AF: 0.763 Hom.: 22177

Bravo AF: 0.634

Asia WGS AF: 0.638 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.81
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2089739; hg19: chr3-161878713;