rs1626340

Positions:

• chr9-99161090-G-A
• chr9-99161090-G-T

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 0.246 in 151,786 control chromosomes in the GnomAD database, including 4,882 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 (4882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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: 0.246 AC: 37277 AN: 151668 Hom.: 4864 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.246 AC: 37339 AN: 151786 Hom.: 4882 Cov.: 32 AF XY: 0.243 AC XY: 18054 AN XY: 74176

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.237

Alfa AF: 0.114 Hom.: 178

Bravo AF: 0.253

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.6
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1626340; hg19: chr9-101923372;