5-135021015-T-G

Variant names:

• chr5-135021015-T-G
• rs526896

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.271 in 152,128 control chromosomes in the GnomAD database, including 5,953 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 0.27 (5953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.271 AC: 41135 AN: 152010 Hom.: 5950 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.271 AC: 41154 AN: 152128 Hom.: 5953 Cov.: 32 AF XY: 0.273 AC XY: 20281 AN XY: 74358

African (AFR) AF: 0.209 AC: 8684 AN: 41494

American (AMR) AF: 0.305 AC: 4660 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3466

East Asian (EAS) AF: 0.488 AC: 2522 AN: 5168

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2627 AN: 10602

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18921 AN: 67970

Other (OTH) AF: 0.263 AC: 556 AN: 2112

Alfa AF: 0.278 Hom.: 19648

Bravo AF: 0.270

Asia WGS AF: 0.475 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Uncertain	23
DANN	Benign	0.75
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs526896; hg19: chr5-134356705; COSMIC: COSV60199590;