rs6468418

Variant names:

• chr8-37611531-T-C
• rs6468418
• ENST00000517714.1:n.136-8112A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-37611531-T-C
• chr8-37611531-T-G

Variant summary

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

The ENST00000517714.1(LINC01605):​n.136-8112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,020 control chromosomes in the GnomAD database, including 20,451 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 0.52 (20451 hom., cov: 32)
• Consequence: LINC01605 ENST00000517714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 3 publications found

Genes affected

LINC01605 (HGNC:51654): (long intergenic non-protein coding RNA 1605)

LOC105379380 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379380	XR_949685.3	n.272-8112A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01605	ENST00000517714.1	n.136-8112A>G		intron_variant	Intron 1 of 4	4
LINC01605	ENST00000784043.1	n.250-8112A>G		intron_variant	Intron 1 of 9
LINC01605	ENST00000784117.1	n.248-8112A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78652 AN: 151902 Hom.: 20433 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.518 AC: 78709 AN: 152020 Hom.: 20451 Cov.: 32 AF XY: 0.523 AC XY: 38848 AN XY: 74312

African (AFR) AF: 0.489 AC: 20288 AN: 41454

American (AMR) AF: 0.517 AC: 7905 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3117 AN: 5152

South Asian (SAS) AF: 0.547 AC: 2637 AN: 4822

European-Finnish (FIN) AF: 0.567 AC: 5983 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35579 AN: 67958

Other (OTH) AF: 0.500 AC: 1055 AN: 2108

Alfa AF: 0.516 Hom.: 34415

Bravo AF: 0.513

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.67
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6468418; hg19: chr8-37469049;