3-5368724-C-T

Variant names:

• chr3-5368724-C-T
• rs10510303

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 0.256 in 151,984 control chromosomes in the GnomAD database, including 7,965 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 0.26 (7965 hom., cov: 33)
• Consequence: LOC124906205 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 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: 0.256 AC: 38820 AN: 151864 Hom.: 7940 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.256 AC: 38888 AN: 151984 Hom.: 7965 Cov.: 33 AF XY: 0.259 AC XY: 19248 AN XY: 74286

African (AFR) AF: 0.554 AC: 22944 AN: 41418

American (AMR) AF: 0.317 AC: 4840 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3466

East Asian (EAS) AF: 0.225 AC: 1165 AN: 5186

South Asian (SAS) AF: 0.193 AC: 932 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1594 AN: 10546

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.0953 AC: 6481 AN: 67972

Other (OTH) AF: 0.217 AC: 458 AN: 2108

Alfa AF: 0.156 Hom.: 4939

Bravo AF: 0.285

Asia WGS AF: 0.252 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.0
DANN	Benign	0.58
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10510303; hg19: chr3-5410409;