chr3-1856289-T-C

Variant names:

• chr3-1856289-T-C
• rs2727943

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.778 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

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.813

Alfa AF: 0.830 Hom.: 65140

Bravo AF: 0.775

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2727943; hg19: chr3-1897973;