rs17075255

Variant names:

• chr5-165332102-C-T
• rs17075255

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 0.2 in 151,888 control chromosomes in the GnomAD database, including 3,131 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 0.20 (3131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 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: 0.200 AC: 30411 AN: 151770 Hom.: 3126 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.200 AC: 30445 AN: 151888 Hom.: 3131 Cov.: 32 AF XY: 0.195 AC XY: 14453 AN XY: 74260

African (AFR) AF: 0.204 AC: 8461 AN: 41434

American (AMR) AF: 0.150 AC: 2294 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3462

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5166

South Asian (SAS) AF: 0.103 AC: 497 AN: 4810

European-Finnish (FIN) AF: 0.166 AC: 1759 AN: 10574

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14935 AN: 67892

Other (OTH) AF: 0.200 AC: 420 AN: 2100

Alfa AF: 0.208 Hom.: 2089

Bravo AF: 0.203

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.69
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs17075255; hg19: chr5-164759108;