8-124944074-C-T

Variant names:

• chr8-124944074-C-T
• rs10505452
• ENST00000510897.7:n.1475C>T

Variant summary

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

The ENST00000510897.7(LINC00964):​n.1475C>T 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 0.0687 in 152,240 control chromosomes in the GnomAD database, including 832 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 0.069 (832 hom., cov: 32)
  • Exomes 𝑓: 0.019 (0 hom.)
• Consequence: LINC00964 ENST00000510897.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 2 publications found

Genes affected

LINC00964 (HGNC:27226): (long intergenic non-protein coding RNA 964)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510897.7. 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
	LINC00964	NR_027321.1		n.1522C>T		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00964	ENST00000510897.7	TSL:1	n.1475C>T		non_coding_transcript_exon	Exon 2 of 4
	LINC00964	ENST00000655947.1		n.163C>T		non_coding_transcript_exon	Exon 1 of 4
	LINC00964	ENST00000661433.1		n.720C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10409 AN: 152016 Hom.: 815 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.00990

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00782

Gnomad OTH AF: 0.0828

GnomAD4 exome AF: 0.0192 AC: 2 AN: 104 Hom.: 0 Cov.: 0 AF XY: 0.0286 AC XY: 2 AN XY: 70

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0128 AC: 1 AN: 78

Other (OTH) AF: 0.00 AC: 0 AN: 10

GnomAD4 genome AF: 0.0687 AC: 10452 AN: 152136 Hom.: 832 Cov.: 32 AF XY: 0.0724 AC XY: 5384 AN XY: 74380

African (AFR) AF: 0.114 AC: 4736 AN: 41494

American (AMR) AF: 0.206 AC: 3144 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1148 AN: 5154

South Asian (SAS) AF: 0.0836 AC: 401 AN: 4796

European-Finnish (FIN) AF: 0.00990 AC: 105 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.00779 AC: 530 AN: 68004

Other (OTH) AF: 0.0923 AC: 195 AN: 2112

Alfa AF: 0.0673 Hom.: 446

Bravo AF: 0.0899

Asia WGS AF: 0.207 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.41
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10505452;

hg19: chr8-125956316;