chr14-56647667-G-A

Position:

• chr14-56647667-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017799.4(TMEM260):​c.*170G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 675,144 control chromosomes in the GnomAD database, including 3,491 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 0.11 (1449 hom., cov: 33)
  • Exomes 𝑓: 0.069 (2042 hom.)
• Consequence: TMEM260 NM_017799.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM260	NM_017799.4	c.*170G>A		3_prime_UTR_variant	16/16	ENST00000261556.11	NP_060269.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM260	ENST00000261556.11	c.*170G>A		3_prime_UTR_variant	16/16	2	NM_017799.4	ENSP00000261556	P1
	ENST00000555924.1	n.40+952C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17230 AN: 152008 Hom.: 1439 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0831

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.0898

GnomAD4 exome AF: 0.0686 AC: 35866 AN: 523018 Hom.: 2042 Cov.: 7 AF XY: 0.0676 AC XY: 18104 AN XY: 267798

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.0758

Gnomad4 EAS exome AF: 0.246

Gnomad4 SAS exome AF: 0.0687

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.0438

Gnomad4 OTH exome AF: 0.0852

GnomAD4 genome AF: 0.113 AC: 17262 AN: 152126 Hom.: 1449 Cov.: 33 AF XY: 0.117 AC XY: 8682 AN XY: 74372

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0831

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.0701

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0478

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.0613 Hom.: 435

Bravo AF: 0.123

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.47

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: rs4901706; hg19: chr14-57114385;