rs713251

Variant names:

• chr10-96528309-C-G
• rs713251
• NM_020123.4:c.1395-132G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-96528309-C-G
• chr10-96528309-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 0 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: 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).

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.1395-132G>C		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.1395-132G>C		intron	N/A	ENSP00000360184.4
	TM9SF3	ENST00000852770.1		c.1395-132G>C		intron	N/A	ENSP00000522829.1
	TM9SF3	ENST00000922471.1		c.1392-132G>C		intron	N/A	ENSP00000592530.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000162 AC: 1 AN: 617730 Hom.: 0 AF XY: 0.00000316 AC XY: 1 AN XY: 316480

African (AFR) AF: 0.00 AC: 0 AN: 14220

American (AMR) AF: 0.00 AC: 0 AN: 16754

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13624

East Asian (EAS) AF: 0.00 AC: 0 AN: 29776

South Asian (SAS) AF: 0.0000270 AC: 1 AN: 37038

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30014

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2672

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 443416

Other (OTH) AF: 0.00 AC: 0 AN: 30216

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
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

Other links and lift over

dbSNP: rs713251; hg19: chr10-98288066;