ENST00000400362.5:n.4578T>A

Variant names:

• chr21-45294777-T-A
• rs7279250
• ENST00000400362.5:n.4578T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400362.5(LINC00205):​n.4578T>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 0.574 in 152,136 control chromosomes in the GnomAD database, including 25,782 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 0.57 (25779 hom., cov: 33)
  • Exomes 𝑓: 0.56 (3 hom.)
• Consequence: LINC00205 ENST00000400362.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 2 publications found

Genes affected

LINC00205 (HGNC:16420): (long intergenic non-protein coding RNA 205)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00205	NR_026943.1	n.4588T>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00205	ENST00000400362.5	n.4578T>A		non_coding_transcript_exon_variant	Exon 3 of 3	1
LINC00205	ENST00000454115.8	n.3400+1255T>A		intron_variant	Intron 3 of 3	1
LINC00205	ENST00000647108.1	n.3244+1255T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87269 AN: 152004 Hom.: 25761 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.563 AC: 9 AN: 16 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.574 AC: 87332 AN: 152120 Hom.: 25779 Cov.: 33 AF XY: 0.583 AC XY: 43356 AN XY: 74368

African (AFR) AF: 0.462 AC: 19152 AN: 41498

American (AMR) AF: 0.639 AC: 9779 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3871 AN: 5166

South Asian (SAS) AF: 0.631 AC: 3042 AN: 4822

European-Finnish (FIN) AF: 0.686 AC: 7270 AN: 10600

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40628 AN: 67958

Other (OTH) AF: 0.566 AC: 1193 AN: 2106

Alfa AF: 0.583 Hom.: 3275

Bravo AF: 0.566

Asia WGS AF: 0.692 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.53
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs7279250; hg19: chr21-46714692;