chr10-96567509-T-C

Variant names:

• chr10-96567509-T-C
• rs9633703
• NM_020123.4:c.299-2083A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020123.4(TM9SF3):​c.299-2083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,054 control chromosomes in the GnomAD database, including 28,006 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 0.59 (28006 hom., cov: 32)
• Consequence: TM9SF3 NM_020123.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

Genes affected

TM9SF3 (HGNC:21529): (transmembrane 9 superfamily member 3) Predicted to be involved in protein localization to membrane. Predicted to be located in exocytic vesicle. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020123.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TM9SF3	NM_020123.4	MANE Select	c.299-2083A>G		intron	N/A	NP_064508.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TM9SF3	ENST00000371142.9	TSL:1 MANE Select	c.299-2083A>G		intron	N/A	ENSP00000360184.4	Q9HD45
	TM9SF3	ENST00000852770.1		c.299-2083A>G		intron	N/A	ENSP00000522829.1
	TM9SF3	ENST00000922471.1		c.299-2083A>G		intron	N/A	ENSP00000592530.1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89354 AN: 151936 Hom.: 27989 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.588 AC: 89396 AN: 152054 Hom.: 28006 Cov.: 32 AF XY: 0.593 AC XY: 44087 AN XY: 74330

African (AFR) AF: 0.371 AC: 15364 AN: 41442

American (AMR) AF: 0.581 AC: 8880 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2255 AN: 3472

East Asian (EAS) AF: 0.826 AC: 4280 AN: 5180

South Asian (SAS) AF: 0.728 AC: 3511 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7498 AN: 10562

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45424 AN: 67972

Other (OTH) AF: 0.597 AC: 1258 AN: 2108

Alfa AF: 0.650 Hom.: 16628

Bravo AF: 0.567

Asia WGS AF: 0.725 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.63
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9633703; hg19: chr10-98327266;