rs9332392

Variant names:

• chr7-19751353-T-A
• rs9332392
• NM_001363562.2:c.147+21197A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-19751353-T-A
• chr7-19751353-T-C
• chr7-19751353-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001363562.2(TMEM196):​c.147+21197A>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: TMEM196 NM_001363562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 1 publications found

Genes affected

TMEM196 (HGNC:22431): (transmembrane protein 196) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC107986774 (HGNC:):

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=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM196	NM_001363562.2	c.147+21197A>T		intron_variant	Intron 1 of 4	ENST00000405844.6	NP_001350491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM196	ENST00000405844.6	c.147+21197A>T		intron_variant	Intron 1 of 4	5	NM_001363562.2	ENSP00000385087.2
TMEM196	ENST00000405764.7	c.147+21197A>T		intron_variant	Intron 1 of 3	1		ENSP00000384234.3
TMEM196	ENST00000422233.5	c.-57-21915A>T		intron_variant	Intron 1 of 4	5		ENSP00000414247.1
TMEM196	ENST00000493519.2	c.-58+21749A>T		intron_variant	Intron 1 of 3	5		ENSP00000438368.1

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	-0.82
CADD	Benign	8.2
DANN	Benign	0.41
PhyloP100		0.80

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: rs9332392; hg19: chr7-19790976;