rs395660

Variant names:

• chr14-36063593-C-T
• rs395660
• ENST00000546376.1:n.482G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000257826 ENST00000546376.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 1 publications found

Genes affected

ENSG00000257826 (HGNC:):

LINC00609 (HGNC:43960): (long intergenic non-protein coding RNA 609)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105370452	XR_943752.3	n.742+3395G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257826	ENST00000546376.1	n.482G>A		non_coding_transcript_exon_variant	Exon 2 of 3	2
LINC00609	ENST00000550089.2	n.464-91C>T		intron_variant	Intron 3 of 4	3
LINC00609	ENST00000660969.2	n.516-91C>T		intron_variant	Intron 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.443 AC: 18364 AN: 41440

American (AMR) AF: 0.361 AC: 5518 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1535 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2044 AN: 5176

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3813 AN: 10542

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25539 AN: 67960

Other (OTH) AF: 0.408 AC: 862 AN: 2114

Alfa AF: 0.383 Hom.: 1441

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs395660; hg19: chr14-36532799;