chr8-37592483-T-C

Variant names:

• chr8-37592483-T-C
• rs7821974
• ENST00000517363.2:n.34+6578A>G

Variant summary

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

The ENST00000517363.2(LINC01605):​n.34+6578A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,026 control chromosomes in the GnomAD database, including 6,461 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 0.22 (6461 hom., cov: 32)
• Consequence: LINC01605 ENST00000517363.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01605	NR_170186.1	n.779+6578A>G		intron_variant	Intron 1 of 4
LINC01605	NR_170187.1	n.779+6578A>G		intron_variant	Intron 1 of 6
LINC01605	NR_170188.1	n.779+6578A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01605	ENST00000517363.2	n.34+6578A>G		intron_variant	Intron 1 of 7	3
LINC01605	ENST00000783999.1	n.338+6578A>G		intron_variant	Intron 1 of 4
LINC01605	ENST00000784000.1	n.34+6578A>G		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33157 AN: 151906 Hom.: 6435 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33227 AN: 152026 Hom.: 6461 Cov.: 32 AF XY: 0.219 AC XY: 16246 AN XY: 74344

African (AFR) AF: 0.490 AC: 20277 AN: 41376

American (AMR) AF: 0.228 AC: 3484 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2596 AN: 5162

South Asian (SAS) AF: 0.141 AC: 682 AN: 4820

European-Finnish (FIN) AF: 0.0693 AC: 735 AN: 10606

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0675 AC: 4587 AN: 67990

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.119 Hom.: 9284

Bravo AF: 0.246

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.79
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7821974; hg19: chr8-37450001;