rs4634268

Positions:

• chr4-188569184-C-T

Variant summary

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

The NR_033869.1(LINC01060):​n.343-32584C>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 0.969 in 152,334 control chromosomes in the GnomAD database, including 71,577 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 0.97 (71577 hom., cov: 33)
• Consequence: LINC01060 NR_033869.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

ACMG classification

Verdict is Benign. Variant got -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 = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01060	NR_033869.1	n.343-32584C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000664177.1	n.330+83319C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147557 AN: 152216 Hom.: 71520 Cov.: 33

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.984

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.975

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

GnomAD4 genome AF: 0.969 AC: 147673 AN: 152334 Hom.: 71577 Cov.: 33 AF XY: 0.971 AC XY: 72366 AN XY: 74500

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.984

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.975

Alfa AF: 0.969 Hom.: 8856

Bravo AF: 0.968

Asia WGS AF: 0.995 AC: 3460 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	0.097
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4634268; hg19: chr4-189490338;