chr5-131147615-T-A

Variant names:

• chr5-131147615-T-A
• rs2189663

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.39 in 152,034 control chromosomes in the GnomAD database, including 15,000 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 0.39 (15000 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 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: 0.390 AC: 59175 AN: 151914 Hom.: 14961 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.390 AC: 59256 AN: 152034 Hom.: 15000 Cov.: 31 AF XY: 0.385 AC XY: 28597 AN XY: 74338

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.350

Alfa AF: 0.331 Hom.: 1277

Bravo AF: 0.400

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2189663; hg19: chr5-130483308;