rs2275959

Variant names:

• chr8-37597541-G-A
• rs2275959
• ENST00000519691.2:n.2321C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-37597541-G-A
• chr8-37597541-G-C
• chr8-37597541-G-T

Variant summary

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

The ENST00000784537.1(LINC01605):​n.2038C>T 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 0.451 in 388,260 control chromosomes in the GnomAD database, including 41,194 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 0.42 (14180 hom., cov: 33)
  • Exomes 𝑓: 0.47 (27014 hom.)
• Consequence: LINC01605 ENST00000784537.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 16 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01605	NR_170186.1		n.779+1520C>T		intron	N/A
	LINC01605	NR_170187.1		n.779+1520C>T		intron	N/A
	LINC01605	NR_170188.1		n.779+1520C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01605	ENST00000519691.2	TSL:6	n.2321C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC01605	ENST00000784537.1		n.2038C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC01605	ENST00000784538.1		n.997C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63589 AN: 151962 Hom.: 14176 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.473 AC: 111631 AN: 236180 Hom.: 27014 Cov.: 0 AF XY: 0.476 AC XY: 62934 AN XY: 132312

African (AFR) AF: 0.252 AC: 1578 AN: 6254

American (AMR) AF: 0.484 AC: 8295 AN: 17122

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 2713 AN: 6788

East Asian (EAS) AF: 0.441 AC: 3782 AN: 8572

South Asian (SAS) AF: 0.491 AC: 23545 AN: 47984

European-Finnish (FIN) AF: 0.551 AC: 5553 AN: 10076

Middle Eastern (MID) AF: 0.373 AC: 338 AN: 906

European-Non Finnish (NFE) AF: 0.477 AC: 60673 AN: 127318

Other (OTH) AF: 0.462 AC: 5154 AN: 11160

GnomAD4 genome AF: 0.418 AC: 63615 AN: 152080 Hom.: 14180 Cov.: 33 AF XY: 0.426 AC XY: 31677 AN XY: 74330

African (AFR) AF: 0.261 AC: 10833 AN: 41468

American (AMR) AF: 0.472 AC: 7211 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2263 AN: 5176

South Asian (SAS) AF: 0.482 AC: 2326 AN: 4824

European-Finnish (FIN) AF: 0.552 AC: 5833 AN: 10562

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32286 AN: 67972

Other (OTH) AF: 0.426 AC: 901 AN: 2114

Alfa AF: 0.450 Hom.: 11963

Bravo AF: 0.405

Asia WGS AF: 0.427 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.097

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2275959;

hg19: chr8-37455059;

COSMIC: COSV72906546;