chr17-75010901-C-T

Variant names:

• chr17-75010901-C-T
• rs9907177

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 0.252 in 151,992 control chromosomes in the GnomAD database, including 5,994 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 0.25 (5994 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.386 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: 0.253 AC: 38361 AN: 151874 Hom.: 5994 Cov.: 31

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.252 AC: 38361 AN: 151992 Hom.: 5994 Cov.: 31 AF XY: 0.257 AC XY: 19090 AN XY: 74282

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.280

Alfa AF: 0.310 Hom.: 15369

Bravo AF: 0.245

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9907177; hg19: chr17-73006996;