rs1412340

Variant names:

• chr9-31619336-G-A
• rs1412340

Your query was ambiguous. Multiple possible variants found:

• chr9-31619336-G-A
• chr9-31619336-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 0.293 in 151,838 control chromosomes in the GnomAD database, including 6,789 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 0.29 (6789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.293 AC: 44477 AN: 151720 Hom.: 6778 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.293 AC: 44510 AN: 151838 Hom.: 6789 Cov.: 32 AF XY: 0.293 AC XY: 21738 AN XY: 74196

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.308

Alfa AF: 0.241 Hom.: 1128

Bravo AF: 0.305

Asia WGS AF: 0.176 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412340; hg19: chr9-31619334;