chr14-56577287-T-C

Variant names:

• chr14-56577287-T-C
• rs1959064
• ENST00000556810.5:c.50-7714T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556810.5(TMEM260):​c.50-7714T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,952 control chromosomes in the GnomAD database, including 6,989 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 0.27 (6989 hom., cov: 31)
• Consequence: TMEM260 ENST00000556810.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 3 publications found

Genes affected

TMEM260 (HGNC:20185): (transmembrane protein 260) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM260 Gene-Disease associations (from GenCC):

• structural heart defects and renal anomalies syndrome

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556810.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM260	ENST00000556810.5	TSL:3	c.50-7714T>C		intron	N/A	ENSP00000451677.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41074 AN: 151834 Hom.: 6984 Cov.: 31

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.270 AC: 41083 AN: 151952 Hom.: 6989 Cov.: 31 AF XY: 0.277 AC XY: 20600 AN XY: 74244

African (AFR) AF: 0.0667 AC: 2766 AN: 41478

American (AMR) AF: 0.428 AC: 6530 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3466

East Asian (EAS) AF: 0.499 AC: 2574 AN: 5154

South Asian (SAS) AF: 0.286 AC: 1378 AN: 4816

European-Finnish (FIN) AF: 0.397 AC: 4174 AN: 10524

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21814 AN: 67944

Other (OTH) AF: 0.289 AC: 608 AN: 2102

Alfa AF: 0.301 Hom.: 3770

Bravo AF: 0.267

Asia WGS AF: 0.367 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1959064; hg19: chr14-57044005;