5-136018635-T-A

Variant names:

• chr5-136018635-T-A
• rs4976360

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 0.427 in 152,012 control chromosomes in the GnomAD database, including 15,295 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 0.43 (15295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 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: 0.427 AC: 64860 AN: 151894 Hom.: 15297 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.427 AC: 64874 AN: 152012 Hom.: 15295 Cov.: 32 AF XY: 0.424 AC XY: 31483 AN XY: 74298

African (AFR) AF: 0.233 AC: 9664 AN: 41468

American (AMR) AF: 0.429 AC: 6545 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1212 AN: 5178

South Asian (SAS) AF: 0.393 AC: 1890 AN: 4812

European-Finnish (FIN) AF: 0.515 AC: 5442 AN: 10558

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36917 AN: 67942

Other (OTH) AF: 0.429 AC: 903 AN: 2106

Alfa AF: 0.469 Hom.: 2160

Bravo AF: 0.410

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.9
DANN	Benign	0.45
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs4976360; hg19: chr5-135354324;