rs9326798

Positions:

• chr5-110322927-G-A
• chr5-110322927-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 0.0317 in 152,200 control chromosomes in the GnomAD database, including 153 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 0.032 (153 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

Genes affected

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.110322927G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM232	ENST00000507188.6	n.1308+307C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4822 AN: 152082 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00584

Gnomad OTH AF: 0.0269

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

GnomAD4 genome AF: 0.0317 AC: 4826 AN: 152200 Hom.: 153 Cov.: 32 AF XY: 0.0321 AC XY: 2390 AN XY: 74416

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00584

Gnomad4 OTH AF: 0.0266

Alfa AF: 0.00393 Hom.: 1

Bravo AF: 0.0397

Asia WGS AF: 0.0390 AC: 135 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	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9326798; hg19: chr5-109658628;