rs3742575

Positions:

• chr14-56650981-G-A

Variant summary

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

The ENST00000554597.5(ENSG00000259133):​n.370-1853C>T 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 0.266 in 152,060 control chromosomes in the GnomAD database, including 6,888 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 (6888 hom., cov: 32)
• Consequence: ENST00000554597.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM260	XR_007064017.1	n.1987-9558G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000554597.5	n.370-1853C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40456 AN: 151942 Hom.: 6887 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.266 AC: 40445 AN: 152060 Hom.: 6888 Cov.: 32 AF XY: 0.265 AC XY: 19671 AN XY: 74334

Gnomad4 AFR AF: 0.0707

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.254

Alfa AF: 0.315 Hom.: 1048

Bravo AF: 0.247

Asia WGS AF: 0.176 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3742575; hg19: chr14-57117699;