rs17108927

Variant names:

• chr5-148906754-T-C
• rs17108927

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 0.0542 in 152,234 control chromosomes in the GnomAD database, including 269 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 0.054 (269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0951 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: 0.0542 AC: 8248 AN: 152116 Hom.: 266 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0542 AC: 8253 AN: 152234 Hom.: 269 Cov.: 32 AF XY: 0.0530 AC XY: 3945 AN XY: 74436

African (AFR) AF: 0.0976 AC: 4053 AN: 41512

American (AMR) AF: 0.0324 AC: 496 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0253 AC: 88 AN: 3472

East Asian (EAS) AF: 0.0551 AC: 285 AN: 5176

South Asian (SAS) AF: 0.0438 AC: 211 AN: 4818

European-Finnish (FIN) AF: 0.0135 AC: 143 AN: 10624

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0409 AC: 2784 AN: 68022

Other (OTH) AF: 0.0548 AC: 116 AN: 2116

Alfa AF: 0.0478 Hom.: 32

Bravo AF: 0.0596

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.34
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs17108927; hg19: chr5-148286317;