rs7017907

chr8-37550612-A-Cchr8-37550612-A-T

Variant summary

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

The ENST00000519738.5(LINC01605):n.162+3410T>G 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 0.237 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 ENST00000519738.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01605	NR_170186.1	n.780-21422T>G		intron_variant, non_coding_transcript_variant
LINC01605	NR_170187.1	n.915+3410T>G		intron_variant, non_coding_transcript_variant
LINC01605	NR_170188.1	n.915+3410T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01605	ENST00000519738.5	n.162+3410T>G		intron_variant, non_coding_transcript_variant		5
LINC01605	ENST00000517363.1	n.46+3410T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0972

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.223

Alfa AF: 0.150 Hom.: 1278

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7017907; hg19: chr8-37408130;