rs9633703

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-96567509-T-A
• chr10-96567509-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020123.4(TM9SF3):​c.299-2083A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TM9SF3 NM_020123.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TM9SF3	NM_020123.4	c.299-2083A>T		intron_variant	Intron 2 of 14	ENST00000371142.9	NP_064508.3
TM9SF3	XM_011539976.3	c.353-2083A>T		intron_variant	Intron 2 of 14		XP_011538278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TM9SF3	ENST00000371142.9	c.299-2083A>T		intron_variant	Intron 2 of 14	1	NM_020123.4	ENSP00000360184.4
TM9SF3	ENST00000443638.1	c.167-2083A>T		intron_variant	Intron 2 of 6	3		ENSP00000401152.1
TM9SF3	ENST00000464654.1	n.261-2083A>T		intron_variant	Intron 2 of 5	5
TM9SF3	ENST00000649367.1	n.637-2083A>T		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs9633703; hg19: chr10-98327266;