ENST00000517363.2:n.438+3410T>G

Variant names:

• chr8-37550612-A-C
• rs7017907
• ENST00000517363.2:n.438+3410T>G

Variant summary

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

The ENST00000517363.2(LINC01605):​n.438+3410T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,000 control chromosomes in the GnomAD database, including 6,215 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 0.24 (6215 hom., cov: 32)
• Consequence: LINC01605 ENST00000517363.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01605	NR_170186.1	n.780-21422T>G		intron_variant	Intron 1 of 4
LINC01605	NR_170187.1	n.915+3410T>G		intron_variant	Intron 2 of 6
LINC01605	NR_170188.1	n.915+3410T>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01605	ENST00000517363.2	n.438+3410T>G		intron_variant	Intron 3 of 7	3
LINC01605	ENST00000519738.5	n.162+3410T>G		intron_variant	Intron 1 of 5	5
LINC01605	ENST00000783999.1	n.339-33656T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35907 AN: 151882 Hom.: 6191 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.237 AC: 35979 AN: 152000 Hom.: 6215 Cov.: 32 AF XY: 0.238 AC XY: 17672 AN XY: 74292

African (AFR) AF: 0.456 AC: 18900 AN: 41416

American (AMR) AF: 0.260 AC: 3966 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5164

South Asian (SAS) AF: 0.182 AC: 877 AN: 4816

European-Finnish (FIN) AF: 0.0972 AC: 1028 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7518 AN: 67972

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.145 Hom.: 1557

Bravo AF: 0.260

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7017907; hg19: chr8-37408130;