3-5368679-C-T

Variant names:

• chr3-5368679-C-T
• rs4143244

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 0.645 in 152,000 control chromosomes in the GnomAD database, including 32,017 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 0.65 (32017 hom., cov: 33)
• Consequence: LOC124906205 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 1 publications found

Genes affected

LOC124906205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.693 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: 0.645 AC: 98005 AN: 151882 Hom.: 31998 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.645 AC: 98080 AN: 152000 Hom.: 32017 Cov.: 33 AF XY: 0.639 AC XY: 47480 AN XY: 74286

African (AFR) AF: 0.592 AC: 24551 AN: 41444

American (AMR) AF: 0.704 AC: 10752 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2035 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2614 AN: 5176

South Asian (SAS) AF: 0.477 AC: 2294 AN: 4812

European-Finnish (FIN) AF: 0.641 AC: 6752 AN: 10534

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47024 AN: 67974

Other (OTH) AF: 0.623 AC: 1317 AN: 2114

Alfa AF: 0.674 Hom.: 100976

Bravo AF: 0.652

Asia WGS AF: 0.503 AC: 1749 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.7
DANN	Benign	0.54
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs4143244; hg19: chr3-5410364;