5-132026085-C-A

Variant names:

• chr5-132026085-C-A
• rs17674015

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 0.291 in 152,156 control chromosomes in the GnomAD database, including 6,969 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 0.29 (6969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 16 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 (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.291 AC: 44256 AN: 152038 Hom.: 6967 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.291 AC: 44273 AN: 152156 Hom.: 6969 Cov.: 32 AF XY: 0.279 AC XY: 20726 AN XY: 74400

African (AFR) AF: 0.267 AC: 11083 AN: 41482

American (AMR) AF: 0.289 AC: 4422 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3472

East Asian (EAS) AF: 0.00250 AC: 13 AN: 5190

South Asian (SAS) AF: 0.0976 AC: 471 AN: 4826

European-Finnish (FIN) AF: 0.229 AC: 2434 AN: 10606

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23851 AN: 67968

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.315 Hom.: 10037

Bravo AF: 0.299

Asia WGS AF: 0.0580 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs17674015; hg19: chr5-131361778;