chr5-159998517-T-C

Variant names:

• chr5-159998517-T-C
• rs6878309

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 0.232 in 152,144 control chromosomes in the GnomAD database, including 5,219 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 0.23 (5219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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: 0.232 AC: 35206 AN: 152026 Hom.: 5191 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.232 AC: 35284 AN: 152144 Hom.: 5219 Cov.: 32 AF XY: 0.230 AC XY: 17076 AN XY: 74398

African (AFR) AF: 0.414 AC: 17177 AN: 41474

American (AMR) AF: 0.275 AC: 4195 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1425 AN: 5182

South Asian (SAS) AF: 0.210 AC: 1016 AN: 4828

European-Finnish (FIN) AF: 0.0982 AC: 1042 AN: 10610

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9319 AN: 68004

Other (OTH) AF: 0.239 AC: 505 AN: 2112

Alfa AF: 0.174 Hom.: 11113

Bravo AF: 0.254

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.64
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6878309; hg19: chr5-159425524; COSMIC: COSV60222805;