chr3-36984376-T-C

Variant names:

• chr3-36984376-T-C
• rs6789043

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 0.453 in 151,862 control chromosomes in the GnomAD database, including 16,324 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 0.45 (16324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.453 AC: 68687 AN: 151746 Hom.: 16311 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.453 AC: 68733 AN: 151862 Hom.: 16324 Cov.: 31 AF XY: 0.444 AC XY: 32955 AN XY: 74198

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.437

Alfa AF: 0.475 Hom.: 23381

Bravo AF: 0.456

Asia WGS AF: 0.208 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6789043; hg19: chr3-37025867;