chr6-113406128-C-T

Variant names:

• chr6-113406128-C-T
• rs10484461
• ENST00000835174.1:n.160C>T

Variant summary

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

The ENST00000835174.1(ENSG00000308578):​n.160C>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 0.128 in 152,090 control chromosomes in the GnomAD database, including 1,484 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 0.13 (1484 hom., cov: 32)
• Consequence: ENSG00000308578 ENST00000835174.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88
• Publications: 1 publications found

Genes affected

ENSG00000308578 (HGNC:):

LINC02518 (HGNC:53509): (long intergenic non-protein coding RNA 2518)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308578	ENST00000835174.1	n.160C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LINC02518	ENST00000835060.1	n.103+27209G>A		intron_variant	Intron 1 of 2
LINC02518	ENST00000835061.1	n.83+27209G>A		intron_variant	Intron 1 of 3
LINC02518	ENST00000835062.1	n.81+27209G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19383 AN: 151972 Hom.: 1482 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0271

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.128 AC: 19399 AN: 152090 Hom.: 1484 Cov.: 32 AF XY: 0.125 AC XY: 9293 AN XY: 74370

African (AFR) AF: 0.211 AC: 8764 AN: 41468

American (AMR) AF: 0.0672 AC: 1027 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3462

East Asian (EAS) AF: 0.0270 AC: 140 AN: 5186

South Asian (SAS) AF: 0.0940 AC: 454 AN: 4830

European-Finnish (FIN) AF: 0.117 AC: 1233 AN: 10580

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7056 AN: 67970

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.115 Hom.: 201

Bravo AF: 0.126

Asia WGS AF: 0.0830 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.32
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10484461; hg19: chr6-113727330;