7-19761741-A-G

Position:

• chr7-19761741-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.147+10809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,182 control chromosomes in the GnomAD database, including 2,394 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 0.16 (2394 hom., cov: 32)
• Consequence: TMEM196 NM_001363562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM196	NM_001363562.2	c.147+10809T>C		intron_variant		ENST00000405844.6	NP_001350491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM196	ENST00000405844.6	c.147+10809T>C		intron_variant		5	NM_001363562.2	ENSP00000385087.2
TMEM196	ENST00000405764.7	c.147+10809T>C		intron_variant		1		ENSP00000384234.3
TMEM196	ENST00000422233.5	c.-58+11826T>C		intron_variant		5		ENSP00000414247.1
TMEM196	ENST00000493519.2	c.-58+11361T>C		intron_variant		5		ENSP00000438368.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24092 AN: 152064 Hom.: 2387 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.158 AC: 24115 AN: 152182 Hom.: 2394 Cov.: 32 AF XY: 0.162 AC XY: 12085 AN XY: 74406

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.149

Alfa AF: 0.128 Hom.: 735

Bravo AF: 0.171

Asia WGS AF: 0.299 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.58

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: rs10486365; hg19: chr7-19801364;