rs717326

Positions:

• chr9-21958525-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 0.124 in 152,128 control chromosomes in the GnomAD database, including 1,416 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 0.12 (1416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18817 AN: 152010 Hom.: 1414 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.124 AC: 18831 AN: 152128 Hom.: 1416 Cov.: 32 AF XY: 0.127 AC XY: 9466 AN XY: 74358

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.112

Alfa AF: 0.133 Hom.: 648

Bravo AF: 0.137

Asia WGS AF: 0.149 AC: 517 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs717326; hg19: chr9-21958524;