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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906205		n.5368679C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;