dbSNP rs713251: TM9SF3:c.1395-132G>C (chr10-96528309-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020123.4(TM9SF3):c.1395-132G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000162 in 617,730 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)

Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

TM9SF3
NM_020123.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

0 publications found

Variant links:

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]

TM9SF3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TM9SF3	NM_020123.4 link	c.1395-132G>C		intron_variant	Intron 11 of 14	ENST00000371142.9	NP_064508.3	Q9HD45A0A024QYS2
TM9SF3	XM_011539976.3 link	c.1449-132G>C		intron_variant	Intron 11 of 14		XP_011538278.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TM9SF3	ENST00000371142.9 link	c.1395-132G>C	intron_variant	Intron 11 of 14	1	NM_020123.4	ENSP00000360184.4	Q9HD45
TM9SF3	ENST00000649367.1 link	n.1733-132G>C	intron_variant	Intron 11 of 14
TM9SF3	ENST00000485093.1 link	n.-136G>C	upstream_gene_variant		5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000162

AC:

AN:

617730

Hom.:

AF XY:

0.00000316

AC XY:

AN XY:

316480

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

14220

American (AMR)

AF:

0.00

AC:

AN:

16754

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13624

East Asian (EAS)

AF:

0.00

AC:

AN:

29776

South Asian (SAS)

AF:

0.0000270

AC:

AN:

37038

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30014

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2672

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

443416

Other (OTH)

AF:

0.00

AC:

AN:

30216

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.2

(source)

DANN

Benign

0.59

PhyloP100

-1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over