rs359965

Variant names:

• chr2-218976169-G-A
• rs359965
• ENST00000419101.3:n.540G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-218976169-G-A
• chr2-218976169-G-C
• chr2-218976169-G-T

Variant summary

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

The ENST00000419101.3(LINC00608):​n.540G>A 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 0.0538 in 152,242 control chromosomes in the GnomAD database, including 406 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 0.054 (406 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC00608 ENST00000419101.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 4 publications found

Genes affected

LINC00608 (HGNC:27179): (long intergenic non-protein coding RNA 608)

ENSG00000308171 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419101.3. 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
	LINC00608	NR_015390.1		n.-115G>A		upstream_gene	N/A
	LINC00608	NR_024385.1		n.-115G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00608	ENST00000419101.3	TSL:5	n.540G>A		non_coding_transcript_exon	Exon 2 of 3
	LINC00608	ENST00000600415.1	TSL:5	n.151+420G>A		intron	N/A
	LINC00608	ENST00000831985.1		n.105-1313G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8175 AN: 152124 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0454

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0538 AC: 8189 AN: 152242 Hom.: 406 Cov.: 32 AF XY: 0.0568 AC XY: 4226 AN XY: 74440

African (AFR) AF: 0.118 AC: 4913 AN: 41504

American (AMR) AF: 0.0307 AC: 470 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3472

East Asian (EAS) AF: 0.140 AC: 726 AN: 5186

South Asian (SAS) AF: 0.157 AC: 755 AN: 4814

European-Finnish (FIN) AF: 0.0275 AC: 292 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 777 AN: 68028

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0280 Hom.: 713

Bravo AF: 0.0551

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs359965; hg19: chr2-219840891;