chr9-17843596-T-A

Variant names:

• chr9-17843596-T-A
• rs7857826

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 0.471 in 151,630 control chromosomes in the GnomAD database, including 17,363 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 0.47 (17363 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 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: 0.471 AC: 71402 AN: 151512 Hom.: 17360 Cov.: 29

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.471 AC: 71446 AN: 151630 Hom.: 17363 Cov.: 29 AF XY: 0.467 AC XY: 34612 AN XY: 74116

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.485

Alfa AF: 0.286 Hom.: 636

Bravo AF: 0.486

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7857826; hg19: chr9-17843594; COSMIC: COSV60336597;