5-136093951-T-C

Variant names:

• chr5-136093951-T-C
• rs1558095

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 0.437 in 152,052 control chromosomes in the GnomAD database, including 16,353 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 0.44 (16353 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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: 0.438 AC: 66506 AN: 151934 Hom.: 16357 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.437 AC: 66513 AN: 152052 Hom.: 16353 Cov.: 32 AF XY: 0.447 AC XY: 33227 AN XY: 74312

African (AFR) AF: 0.196 AC: 8133 AN: 41486

American (AMR) AF: 0.511 AC: 7806 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3472

East Asian (EAS) AF: 0.685 AC: 3536 AN: 5164

South Asian (SAS) AF: 0.473 AC: 2276 AN: 4812

European-Finnish (FIN) AF: 0.563 AC: 5935 AN: 10542

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35652 AN: 67972

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.499 Hom.: 9990

Bravo AF: 0.421

Asia WGS AF: 0.559 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1558095; hg19: chr5-135429640;