3-5365475-A-C

Variant names:

• chr3-5365475-A-C
• rs2323138

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 0.416 in 152,078 control chromosomes in the GnomAD database, including 16,379 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 0.42 (16379 hom., cov: 32)
• Consequence: LOC124906205 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63250 AN: 151960 Hom.: 16374 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.416 AC: 63262 AN: 152078 Hom.: 16379 Cov.: 32 AF XY: 0.406 AC XY: 30145 AN XY: 74302

African (AFR) AF: 0.119 AC: 4927 AN: 41540

American (AMR) AF: 0.416 AC: 6338 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1491 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4824

European-Finnish (FIN) AF: 0.491 AC: 5175 AN: 10536

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40864 AN: 67960

Other (OTH) AF: 0.428 AC: 905 AN: 2114

Alfa AF: 0.285 Hom.: 719

Bravo AF: 0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.87
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs2323138; hg19: chr3-5407160;