rs2390155

Positions:

• chr7-19746486-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363562.2(TMEM196):​c.148-17048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,120 control chromosomes in the GnomAD database, including 21,131 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 0.48 (21131 hom., cov: 32)
• Consequence: TMEM196 NM_001363562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM196	NM_001363562.2	c.148-17048T>C		intron_variant		ENST00000405844.6
LOC107986774	XR_001745112.2	n.1125+23344A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM196	ENST00000405844.6	c.148-17048T>C		intron_variant		5	NM_001363562.2
TMEM196	ENST00000405764.7	c.148-17048T>C		intron_variant		1		P1
TMEM196	ENST00000422233.5	c.-57-17048T>C		intron_variant		5
TMEM196	ENST00000493519.2	c.-57-17048T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73045 AN: 152002 Hom.: 21095 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.481 AC: 73135 AN: 152120 Hom.: 21131 Cov.: 32 AF XY: 0.485 AC XY: 36086 AN XY: 74380

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.444

Alfa AF: 0.355 Hom.: 13810

Bravo AF: 0.508

Asia WGS AF: 0.702 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.28

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: rs2390155; hg19: chr7-19786109;