14-56577287-T-C

Variant names:

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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM260	ENST00000556810.5	c.50-7714T>C		intron_variant	Intron 2 of 3	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;