chr5-136088663-G-A

Variant names:

• chr5-136088663-G-A
• rs6596283

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 0.0714 in 152,224 control chromosomes in the GnomAD database, including 435 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 0.071 (435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10858 AN: 152106 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0714 AC: 10865 AN: 152224 Hom.: 435 Cov.: 32 AF XY: 0.0699 AC XY: 5201 AN XY: 74428

African (AFR) AF: 0.0765 AC: 3176 AN: 41534

American (AMR) AF: 0.0627 AC: 959 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.0936 AC: 485 AN: 5182

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4824

European-Finnish (FIN) AF: 0.0508 AC: 539 AN: 10600

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0725 AC: 4930 AN: 68010

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.0703 Hom.: 862

Bravo AF: 0.0726

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.41
DANN	Benign	0.79
PhyloP100		-1.0

Splicing

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

Publications

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Other links and lift over

dbSNP: rs6596283; hg19: chr5-135424352; COSMIC: COSV107163594;