rs1626340

Variant names:

• chr9-99161090-G-A
• rs1626340

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.299 AC: 12353 AN: 41356

American (AMR) AF: 0.253 AC: 3868 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2420 AN: 5170

South Asian (SAS) AF: 0.230 AC: 1108 AN: 4808

European-Finnish (FIN) AF: 0.154 AC: 1622 AN: 10512

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14544 AN: 67890

Other (OTH) AF: 0.237 AC: 501 AN: 2110

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1626340; hg19: chr9-101923372;