rs4901706

Variant names:

• chr14-56647667-G-A
• rs4901706
• NM_017799.4:c.*170G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-56647667-G-A
• chr14-56647667-G-C
• chr14-56647667-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P

ENSG00000258428 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017799.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM260	NM_017799.4	MANE Select	c.*170G>A		3_prime_UTR	Exon 16 of 16	NP_060269.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM260	ENST00000261556.11	TSL:2 MANE Select	c.*170G>A		3_prime_UTR	Exon 16 of 16	ENSP00000261556.6	Q9NX78-1
	TMEM260	ENST00000539559.6	TSL:1	n.*1204G>A		non_coding_transcript_exon	Exon 15 of 15	ENSP00000442602.2	F5H7D0
	TMEM260	ENST00000556422.5	TSL:1	n.*892G>A		non_coding_transcript_exon	Exon 15 of 15	ENSP00000450988.1	G3V320

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

African (AFR) AF: 0.195 AC: 2253 AN: 11572

American (AMR) AF: 0.181 AC: 2182 AN: 12036

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 992 AN: 13090

East Asian (EAS) AF: 0.246 AC: 6602 AN: 26892

South Asian (SAS) AF: 0.0687 AC: 2505 AN: 36472

European-Finnish (FIN) AF: 0.101 AC: 2817 AN: 27830

Middle Eastern (MID) AF: 0.0713 AC: 151 AN: 2118

European-Non Finnish (NFE) AF: 0.0438 AC: 16020 AN: 365490

Other (OTH) AF: 0.0852 AC: 2344 AN: 27518

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

African (AFR) AF: 0.195 AC: 8099 AN: 41488

American (AMR) AF: 0.153 AC: 2339 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0831 AC: 288 AN: 3464

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5170

South Asian (SAS) AF: 0.0701 AC: 338 AN: 4824

European-Finnish (FIN) AF: 0.109 AC: 1155 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3253 AN: 67994

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.0740 Hom.: 993

Bravo AF: 0.123

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.47
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4901706; hg19: chr14-57114385;