rs17826255

Variant names:

• chr17-31006498-T-C
• rs17826255

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 0.0469 in 152,288 control chromosomes in the GnomAD database, including 319 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 0.047 (319 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 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: 0.0469 AC: 7135 AN: 152170 Hom.: 316 Cov.: 30

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0542

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0469 AC: 7143 AN: 152288 Hom.: 319 Cov.: 30 AF XY: 0.0455 AC XY: 3388 AN XY: 74462

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0620

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.0567 Hom.: 420

Bravo AF: 0.0504

Asia WGS AF: 0.117 AC: 404 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.097

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17826255; hg19: chr17-29333516;