rs395660

chr14-36063593-C-T

Variant summary

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

The ENST00000546376.1(ENSG00000257826):n.482G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,004 control chromosomes in the GnomAD database, including 11,923 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 0.40 (11923 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000546376.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370452	XR_943752.3	n.742+3395G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000546376.1	n.482G>A		non_coding_transcript_exon_variant	2/3	2
	ENST00000700834.1	n.352-91C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60057 AN: 151886 Hom.: 11905 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.403

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.395 AC: 60110 AN: 152004 Hom.: 11923 Cov.: 32 AF XY: 0.393 AC XY: 29190 AN XY: 74290

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.408

Alfa AF: 0.382 Hom.: 1362

Bravo AF: 0.399

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.5
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: rs395660; hg19: chr14-36532799;