5-173168305-C-T

Variant names:

• chr5-173168305-C-T
• rs29784

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 0.395 in 152,016 control chromosomes in the GnomAD database, including 12,508 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 (12508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.395 AC: 59955 AN: 151898 Hom.: 12510 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.395 AC: 59991 AN: 152016 Hom.: 12508 Cov.: 32 AF XY: 0.393 AC XY: 29208 AN XY: 74316

African (AFR) AF: 0.306 AC: 12679 AN: 41462

American (AMR) AF: 0.392 AC: 5981 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1359 AN: 3472

East Asian (EAS) AF: 0.186 AC: 958 AN: 5152

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4820

European-Finnish (FIN) AF: 0.528 AC: 5586 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31050 AN: 67960

Other (OTH) AF: 0.390 AC: 823 AN: 2108

Alfa AF: 0.414 Hom.: 28588

Bravo AF: 0.381

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.62
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs29784; hg19: chr5-172595308;