rs9906155

Positions:

• chr17-77705615-T-C

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 0.0488 in 152,044 control chromosomes in the GnomAD database, including 221 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 0.049 (221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

ACMG classification

Verdict is Benign. Variant got -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 = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7403 AN: 151928 Hom.: 217 Cov.: 32

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0488 AC: 7425 AN: 152044 Hom.: 221 Cov.: 32 AF XY: 0.0469 AC XY: 3484 AN XY: 74298

Gnomad4 AFR AF: 0.0634

Gnomad4 AMR AF: 0.0300

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.0428

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0506

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0500 Hom.: 67

Bravo AF: 0.0501

Asia WGS AF: 0.0460 AC: 163 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	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9906155; hg19: chr17-75701697;