rs4363506

Variant names:

• chr10-127476239-T-C
• rs4363506

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 0.417 in 152,072 control chromosomes in the GnomAD database, including 13,479 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 (13479 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 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: 0.417 AC: 63410 AN: 151954 Hom.: 13463 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.417 AC: 63474 AN: 152072 Hom.: 13479 Cov.: 33 AF XY: 0.416 AC XY: 30943 AN XY: 74360

African (AFR) AF: 0.370 AC: 15343 AN: 41504

American (AMR) AF: 0.476 AC: 7268 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2926 AN: 5168

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4818

European-Finnish (FIN) AF: 0.371 AC: 3915 AN: 10566

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28864 AN: 67952

Other (OTH) AF: 0.430 AC: 907 AN: 2108

Alfa AF: 0.428 Hom.: 46079

Bravo AF: 0.423

Asia WGS AF: 0.532 AC: 1825 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.4
DANN	Benign	0.74
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs4363506; hg19: chr10-129274503;