8-124944074-C-T

Position:

• chr8-124944074-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00964 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00964	NR_027321.1	n.1522C>T		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00964	ENST00000510897.7	n.1475C>T		non_coding_transcript_exon_variant	2/4	1
LINC00964	ENST00000655947.1	n.163C>T		non_coding_transcript_exon_variant	1/4
LINC00964	ENST00000661433.1	n.720C>T		non_coding_transcript_exon_variant	1/3

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0128

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.00990

Gnomad4 NFE AF: 0.00779

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.0724 Hom.: 415

Bravo AF: 0.0899

Asia WGS AF: 0.207 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505452; hg19: chr8-125956316;