3-1856289-T-C

Variant names:

• chr3-1856289-T-C
• rs2727943

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.778 in 151,994 control chromosomes in the GnomAD database, including 46,792 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 0.78 (46792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118154 AN: 151876 Hom.: 46766 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.778 AC: 118225 AN: 151994 Hom.: 46792 Cov.: 32 AF XY: 0.767 AC XY: 56938 AN XY: 74252

African (AFR) AF: 0.729 AC: 30223 AN: 41458

American (AMR) AF: 0.688 AC: 10470 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2557 AN: 5142

South Asian (SAS) AF: 0.605 AC: 2918 AN: 4820

European-Finnish (FIN) AF: 0.748 AC: 7911 AN: 10570

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58221 AN: 67994

Other (OTH) AF: 0.813 AC: 1714 AN: 2108

Alfa AF: 0.823 Hom.: 161354

Bravo AF: 0.775

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2727943; hg19: chr3-1897973;