rs12344488

Variant names:

• chr9-75811009-G-A
• rs12344488

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 0.0554 in 152,190 control chromosomes in the GnomAD database, including 264 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 0.055 (264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

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 (NFE) allele frequency at 95% confidence interval = 0.0687 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: 0.0554 AC: 8422 AN: 152072 Hom.: 263 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0554 AC: 8428 AN: 152190 Hom.: 264 Cov.: 32 AF XY: 0.0522 AC XY: 3885 AN XY: 74414

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0358

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0411

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0667 Hom.: 761

Bravo AF: 0.0572

Asia WGS AF: 0.0210 AC: 73 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12344488; hg19: chr9-78425925;