ENST00000457405.2:n.532+26198C>T

Variant names:

• chr1-168810231-G-A
• rs6659944
• ENST00000457405.2:n.532+26198C>T

Variant summary

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

The ENST00000457405.2(LINC00970):​n.532+26198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,970 control chromosomes in the GnomAD database, including 28,035 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 0.58 (28035 hom., cov: 31)
• Consequence: LINC00970 ENST00000457405.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 4 publications found

Genes affected

LINC00970 (HGNC:):

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000457405.2	n.532+26198C>T		intron_variant	Intron 6 of 7	3
LINC00970	ENST00000650631.1	n.414-62627C>T		intron_variant	Intron 4 of 8
LINC00970	ENST00000715524.1	n.604-77009C>T		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87267 AN: 151852 Hom.: 27971 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.575 AC: 87394 AN: 151970 Hom.: 28035 Cov.: 31 AF XY: 0.582 AC XY: 43252 AN XY: 74264

African (AFR) AF: 0.821 AC: 34052 AN: 41486

American (AMR) AF: 0.585 AC: 8930 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1518 AN: 3458

East Asian (EAS) AF: 0.985 AC: 5103 AN: 5180

South Asian (SAS) AF: 0.611 AC: 2943 AN: 4816

European-Finnish (FIN) AF: 0.523 AC: 5499 AN: 10514

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27675 AN: 67948

Other (OTH) AF: 0.524 AC: 1105 AN: 2108

Alfa AF: 0.454 Hom.: 10792

Bravo AF: 0.591

Asia WGS AF: 0.804 AC: 2793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6659944; hg19: chr1-168779469;