rs12344488

Variant names:

• chr9-75811009-G-A
• rs12344488

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 0.0554 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0515 AC: 2140 AN: 41526

American (AMR) AF: 0.0475 AC: 726 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0358 AC: 124 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0411 AC: 198 AN: 4818

European-Finnish (FIN) AF: 0.0273 AC: 289 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0704 AC: 4786 AN: 67994

Other (OTH) AF: 0.0573 AC: 121 AN: 2110

Alfa AF: 0.0644 Hom.: 1130

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs12344488; hg19: chr9-78425925;