rs1959068

Positions:

• chr14-56532814-A-G
• chr14-56532814-A-T

Variant summary

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

The NR_135241.1(LOC101927690):​n.188-16457A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,134 control chromosomes in the GnomAD database, including 11,724 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 0.38 (11724 hom., cov: 33)
• Consequence: LOC101927690 NR_135241.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64

Genes affected

(HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927690	NR_135241.1	n.188-16457A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000557246.1	n.188-16457A>G		intron_variant, non_coding_transcript_variant		1
TMEM260	ENST00000556810.5	c.49+41233A>G		intron_variant		3		ENSP00000451677

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57444 AN: 152018 Hom.: 11721 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.378 AC: 57460 AN: 152134 Hom.: 11724 Cov.: 33 AF XY: 0.381 AC XY: 28331 AN XY: 74362

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.390

Alfa AF: 0.380 Hom.: 21926

Bravo AF: 0.387

Asia WGS AF: 0.585 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1959068; hg19: chr14-56999532;