chr4-79595695-A-T

Position:

• chr4-79595695-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668018.1(LINC00989):​n.545+10468A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,974 control chromosomes in the GnomAD database, including 34,021 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 0.66 (34021 hom., cov: 32)
• Consequence: LINC00989 ENST00000668018.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

LINC00989 (HGNC:48918): (long intergenic non-protein coding RNA 989)

LOC107986294 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986294	XR_007058155.1	n.228-787A>T		intron_variant, non_coding_transcript_variant
LOC107986294	XR_007058156.1	n.492-787A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00989	ENST00000668018.1	n.545+10468A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100139 AN: 151858 Hom.: 34004 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.659 AC: 100188 AN: 151974 Hom.: 34021 Cov.: 32 AF XY: 0.656 AC XY: 48692 AN XY: 74244

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.690

Alfa AF: 0.639 Hom.: 2214

Bravo AF: 0.659

Asia WGS AF: 0.525 AC: 1827 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031004; hg19: chr4-80516849;