rs2275959

Positions:

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

Variant summary

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

The ENST00000519691.1(ENSG00000254290):​n.2318C>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: ENST00000519691.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01605	NR_170186.1	n.779+1520C>T		intron_variant, non_coding_transcript_variant
LINC01605	NR_170187.1	n.779+1520C>T		intron_variant, non_coding_transcript_variant
LINC01605	NR_170188.1	n.779+1520C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000519691.1	n.2318C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.252

Gnomad4 AMR exome AF: 0.484

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.491

Gnomad4 FIN exome AF: 0.551

Gnomad4 NFE exome AF: 0.477

Gnomad4 OTH exome AF: 0.462

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.426

Alfa AF: 0.447 Hom.: 8825

Bravo AF: 0.405

Asia WGS AF: 0.427 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275959; hg19: chr8-37455059; COSMIC: COSV72906546;