rs6744457

Positions:

• chr2-215685532-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.723+55345G>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 0.215 in 152,096 control chromosomes in the GnomAD database, including 3,780 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 0.22 (3780 hom., cov: 32)
• Consequence: LINC00607 NR_037195.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00607	NR_037195.1	n.723+55345G>A		intron_variant, non_coding_transcript_variant
LOC102724861	XR_001739875.2	n.740+3406C>T		intron_variant, non_coding_transcript_variant
LOC102724861	XR_001739874.2	n.860+2071C>T		intron_variant, non_coding_transcript_variant
LOC102724861	XR_923864.3	n.720+2071C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000417485.6	n.986+3406C>T		intron_variant, non_coding_transcript_variant		5
LINC00607	ENST00000445174.5	n.723+55345G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32735 AN: 151978 Hom.: 3780 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0838

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.215 AC: 32739 AN: 152096 Hom.: 3780 Cov.: 32 AF XY: 0.210 AC XY: 15616 AN XY: 74352

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.226

Alfa AF: 0.235 Hom.: 8977

Bravo AF: 0.213

Asia WGS AF: 0.0550 AC: 194 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	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6744457; hg19: chr2-216550255;