14-56577287-T-C

Position:

• chr14-56577287-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56577287T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM260	ENST00000556810.5	c.50-7714T>C		intron_variant		3		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

Gnomad4 AFR AF: 0.0667

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.289

Alfa AF: 0.300 Hom.: 3381

Bravo AF: 0.267

Asia WGS AF: 0.367 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1959064; hg19: chr14-57044005;