rs9907177

Variant names:

• chr17-75010901-C-T
• rs9907177

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 0.252 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0623 AC: 2586 AN: 41508

American (AMR) AF: 0.395 AC: 6024 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3468

East Asian (EAS) AF: 0.176 AC: 907 AN: 5164

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4812

European-Finnish (FIN) AF: 0.352 AC: 3711 AN: 10546

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21460 AN: 67916

Other (OTH) AF: 0.280 AC: 591 AN: 2114

Alfa AF: 0.296 Hom.: 22359

Bravo AF: 0.245

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs9907177; hg19: chr17-73006996;