rs2680182

Positions:

• chr2-215625359-C-T

Variant summary

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

The NR_037195.1(LINC00607):​n.724-1124G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,170 control chromosomes in the GnomAD database, including 1,126 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 0.11 (1126 hom., cov: 33)
• Consequence: LINC00607 NR_037195.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

Genes affected

(HGNC:):

LINC00607 (HGNC:43944): (long intergenic non-protein coding RNA 607)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00607	NR_037195.1	n.724-1124G>A		intron_variant, non_coding_transcript_variant
LOC102724861	XR_001739875.2	n.274+3434C>T		intron_variant, non_coding_transcript_variant
LOC102724861	XR_001739874.2	n.274+3434C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000417485.6	n.284+3434C>T		intron_variant, non_coding_transcript_variant		5
LINC00607	ENST00000445174.5	n.724-1124G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16858 AN: 152052 Hom.: 1123 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.101

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.111 AC: 16882 AN: 152170 Hom.: 1126 Cov.: 33 AF XY: 0.114 AC XY: 8516 AN XY: 74410

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.0620

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.101

Alfa AF: 0.108 Hom.: 559

Bravo AF: 0.112

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2680182; hg19: chr2-216490082;