8-55744325-A-T

Position:

• chr8-55744325-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001286657.2(TMEM68):​c.749-705T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0035 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TMEM68 NM_001286657.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

TMEM68 (HGNC:26510): (transmembrane protein 68) Predicted to enable acyltransferase activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM68 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM68	NM_001286657.2	c.749-705T>A		intron_variant		ENST00000434581.7	NP_001273586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM68	ENST00000434581.7	c.749-705T>A		intron_variant		5	NM_001286657.2	ENSP00000395204.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 33 AN: 8792 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00270

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00325

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00535

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00252

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00353 AC: 31 AN: 8786 Hom.: 0 Cov.: 0 AF XY: 0.00344 AC XY: 14 AN XY: 4070

Gnomad4 AFR AF: 0.00216

Gnomad4 AMR AF: 0.00325

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00535

Gnomad4 SAS AF: 0.0150

Gnomad4 FIN AF: 0.0118

Gnomad4 NFE AF: 0.00252

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.17

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: rs7836689; hg19: chr8-56656884;