8-37598920-A-G

Variant names:

• chr8-37598920-A-G
• rs2298320
• ENST00000519691.2:n.942T>C

Variant summary

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

The ENST00000519691.2(LINC01605):​n.942T>C 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 0.462 in 166,452 control chromosomes in the GnomAD database, including 18,148 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 0.47 (16817 hom., cov: 32)
  • Exomes 𝑓: 0.41 (1331 hom.)
• Consequence: LINC01605 ENST00000519691.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519691.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01605	NR_170186.1		n.779+141T>C		intron	N/A
	LINC01605	NR_170187.1		n.779+141T>C		intron	N/A
	LINC01605	NR_170188.1		n.779+141T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01605	ENST00000519691.2	TSL:6	n.942T>C		non_coding_transcript_exon	Exon 1 of 1
	LINC01605	ENST00000784554.1		n.60T>C		non_coding_transcript_exon	Exon 2 of 2
	LINC01605	ENST00000517363.2	TSL:3	n.34+141T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70868 AN: 151928 Hom.: 16783 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.412 AC: 5940 AN: 14406 Hom.: 1331 Cov.: 0 AF XY: 0.417 AC XY: 3048 AN XY: 7308

African (AFR) AF: 0.315 AC: 29 AN: 92

American (AMR) AF: 0.397 AC: 516 AN: 1300

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 103 AN: 280

East Asian (EAS) AF: 0.431 AC: 44 AN: 102

South Asian (SAS) AF: 0.367 AC: 581 AN: 1582

European-Finnish (FIN) AF: 0.488 AC: 281 AN: 576

Middle Eastern (MID) AF: 0.407 AC: 22 AN: 54

European-Non Finnish (NFE) AF: 0.421 AC: 4036 AN: 9582

Other (OTH) AF: 0.391 AC: 328 AN: 838

GnomAD4 genome AF: 0.467 AC: 70962 AN: 152046 Hom.: 16817 Cov.: 32 AF XY: 0.473 AC XY: 35144 AN XY: 74304

African (AFR) AF: 0.403 AC: 16716 AN: 41480

American (AMR) AF: 0.486 AC: 7434 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1428 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2404 AN: 5152

South Asian (SAS) AF: 0.493 AC: 2377 AN: 4824

European-Finnish (FIN) AF: 0.562 AC: 5933 AN: 10560

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33076 AN: 67960

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.473 Hom.: 5632

Bravo AF: 0.457

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.83
DANN	Benign	0.60
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2298320; hg19: chr8-37456438;