rs4634268

Variant names:

• chr4-188569184-C-T
• rs4634268
• ENST00000503458.9:n.330-32584C>T

Variant summary

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

The ENST00000503458.9(LINC01060):​n.330-32584C>T variant causes a intron 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 ENST00000503458.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 0 publications found

Genes affected

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

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 = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01060	NR_033869.1	n.343-32584C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000503458.9	n.330-32584C>T		intron_variant	Intron 3 of 3	3
LINC01060	ENST00000503580.1	n.87+83319C>T		intron_variant	Intron 1 of 1	3
LINC01060	ENST00000510005.7	n.387-32584C>T		intron_variant	Intron 4 of 4	2

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

African (AFR) AF: 0.948 AC: 39406 AN: 41570

American (AMR) AF: 0.984 AC: 15064 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3435 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5187 AN: 5188

South Asian (SAS) AF: 0.994 AC: 4800 AN: 4828

European-Finnish (FIN) AF: 0.988 AC: 10503 AN: 10630

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66089 AN: 68022

Other (OTH) AF: 0.975 AC: 2064 AN: 2116

Alfa AF: 0.968 Hom.: 9208

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
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs4634268; hg19: chr4-189490338;