19-21483408-C-T

Variant names:

• chr19-21483408-C-T
• rs2562456
• ENST00000600810.1:n.197-6257C>T

Variant summary

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

The ENST00000600810.1(ENSG00000269237):​n.197-6257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,318 control chromosomes in the GnomAD database, including 45,511 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 0.77 (45452 hom., cov: 33)
  • Exomes 𝑓: 0.84 (59 hom.)
• Consequence: ENSG00000269237 ENST00000600810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 37 publications found

Genes affected

ENSG00000269237 (HGNC:):

LINC00664 (HGNC:44319): (long intergenic non-protein coding RNA 664)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000600810.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000269237	ENST00000600810.1	TSL:3	n.197-6257C>T		intron	N/A	ENSP00000473166.1	M0R3E3
	LINC00664	ENST00000596718.5	TSL:5	n.35C>T		non_coding_transcript_exon	Exon 1 of 14

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117170 AN: 152036 Hom.: 45426 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.774

GnomAD4 exome AF: 0.841 AC: 138 AN: 164 Hom.: 59 Cov.: 0 AF XY: 0.860 AC XY: 117 AN XY: 136

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.833 AC: 120 AN: 144

Other (OTH) AF: 0.875 AC: 7 AN: 8

GnomAD4 genome AF: 0.771 AC: 117244 AN: 152154 Hom.: 45452 Cov.: 33 AF XY: 0.769 AC XY: 57177 AN XY: 74374

African (AFR) AF: 0.847 AC: 35195 AN: 41552

American (AMR) AF: 0.725 AC: 11093 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2885 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3596 AN: 5136

South Asian (SAS) AF: 0.796 AC: 3843 AN: 4826

European-Finnish (FIN) AF: 0.716 AC: 7581 AN: 10592

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50502 AN: 67966

Other (OTH) AF: 0.771 AC: 1629 AN: 2114

Alfa AF: 0.750 Hom.: 131059

Bravo AF: 0.773

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.41
PhyloP100		-1.9

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: rs2562456; hg19: chr19-21666210;