rs2298321

Variant names:

• chr8-37598786-G-A
• rs2298321
• ENST00000519691.2:n.1076C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-37598786-G-A
• chr8-37598786-G-C
• chr8-37598786-G-T

Variant summary

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

The ENST00000519691.2(LINC01605):​n.1076C>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 0.0922 in 268,786 control chromosomes in the GnomAD database, including 1,439 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 0.083 (683 hom., cov: 32)
  • Exomes 𝑓: 0.10 (756 hom.)
• Consequence: LINC01605 ENST00000519691.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01605	NR_170186.1	n.779+275C>T		intron_variant	Intron 1 of 4
LINC01605	NR_170187.1	n.779+275C>T		intron_variant	Intron 1 of 6
LINC01605	NR_170188.1	n.779+275C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01605	ENST00000519691.2	n.1076C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01605	ENST00000784554.1	n.194C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01605	ENST00000517363.2	n.34+275C>T		intron_variant	Intron 1 of 7	3

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12619 AN: 152108 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0809

GnomAD4 exome AF: 0.104 AC: 12167 AN: 116560 Hom.: 756 Cov.: 0 AF XY: 0.110 AC XY: 6915 AN XY: 63026

African (AFR) AF: 0.0177 AC: 29 AN: 1642

American (AMR) AF: 0.0615 AC: 257 AN: 4180

Ashkenazi Jewish (ASJ) AF: 0.0742 AC: 200 AN: 2696

East Asian (EAS) AF: 0.0396 AC: 73 AN: 1842

South Asian (SAS) AF: 0.152 AC: 3550 AN: 23284

European-Finnish (FIN) AF: 0.123 AC: 753 AN: 6112

Middle Eastern (MID) AF: 0.0942 AC: 42 AN: 446

European-Non Finnish (NFE) AF: 0.0952 AC: 6708 AN: 70476

Other (OTH) AF: 0.0944 AC: 555 AN: 5882

GnomAD4 genome AF: 0.0829 AC: 12613 AN: 152226 Hom.: 683 Cov.: 32 AF XY: 0.0858 AC XY: 6386 AN XY: 74432

African (AFR) AF: 0.0212 AC: 882 AN: 41546

American (AMR) AF: 0.0767 AC: 1173 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3468

East Asian (EAS) AF: 0.0670 AC: 347 AN: 5176

South Asian (SAS) AF: 0.185 AC: 893 AN: 4822

European-Finnish (FIN) AF: 0.133 AC: 1406 AN: 10596

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7214 AN: 68006

Other (OTH) AF: 0.0800 AC: 169 AN: 2112

Alfa AF: 0.0966 Hom.: 1283

Bravo AF: 0.0735

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.3
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2298321; hg19: chr8-37456304;