rs2390155

Variant names:

• chr7-19746486-A-G
• rs2390155
• NM_001363562.2:c.148-17048T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363562.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM196	NM_001363562.2	MANE Select	c.148-17048T>C		intron	N/A	NP_001350491.1
	TMEM196	NM_001366625.1		c.166-17048T>C		intron	N/A	NP_001353554.1
	TMEM196	NM_001366626.1		c.166-17048T>C		intron	N/A	NP_001353555.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM196	ENST00000405844.6	TSL:5 MANE Select	c.148-17048T>C		intron	N/A	ENSP00000385087.2
	TMEM196	ENST00000405764.7	TSL:1	c.148-17048T>C		intron	N/A	ENSP00000384234.3
	TMEM196	ENST00000422233.5	TSL:5	c.-57-17048T>C		intron	N/A	ENSP00000414247.1

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

African (AFR) AF: 0.769 AC: 31931 AN: 41508

American (AMR) AF: 0.449 AC: 6861 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5022 AN: 5176

South Asian (SAS) AF: 0.484 AC: 2335 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3409 AN: 10568

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21185 AN: 67986

Other (OTH) AF: 0.444 AC: 937 AN: 2108

Alfa AF: 0.369 Hom.: 19452

Bravo AF: 0.508

Asia WGS AF: 0.702 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.28
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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: rs2390155; hg19: chr7-19786109;