rs9907236

chr17-71493932-G-A

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 0.0416 in 152,228 control chromosomes in the GnomAD database, including 235 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 0.042 (235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 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: 0.0415 AC: 6316 AN: 152112 Hom.: 235 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0416 AC: 6326 AN: 152228 Hom.: 235 Cov.: 32 AF XY: 0.0424 AC XY: 3155 AN XY: 74418

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.00386

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0342

Alfa AF: 0.0199 Hom.: 31

Bravo AF: 0.0438

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.7
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: rs9907236; hg19: chr17-69490073;