rs6744457

Variant names:

• chr2-215685532-C-T
• rs6744457
• NR_187734.1:n.2931C>T

Variant summary

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

The NR_187734.1(LOC102724861):​n.2931C>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 0.215 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: LOC102724861 NR_187734.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 3 publications found

Genes affected

LOC102724861 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187734.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102724861	NR_187734.1		n.2931C>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00607	NR_037195.1		n.723+55345G>A		intron	N/A
	LOC102724861	NR_187735.1		n.740+3406C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237525	ENST00000417485.6	TSL:5	n.986+3406C>T		intron	N/A
	LINC00607	ENST00000417922.2	TSL:4	n.682+15516G>A		intron	N/A
	LINC00607	ENST00000423530.5	TSL:2	n.477-43713G>A		intron	N/A

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

African (AFR) AF: 0.213 AC: 8828 AN: 41470

American (AMR) AF: 0.189 AC: 2893 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5192

South Asian (SAS) AF: 0.0831 AC: 401 AN: 4828

European-Finnish (FIN) AF: 0.233 AC: 2456 AN: 10554

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16524 AN: 67978

Other (OTH) AF: 0.226 AC: 477 AN: 2112

Alfa AF: 0.233 Hom.: 13318

Bravo AF: 0.213

Asia WGS AF: 0.0550 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6744457; hg19: chr2-216550255;