rs1396626

Positions:

• chr1-95559990-G-A
• chr1-95559990-G-T

Variant summary

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

The ENST00000456933.1(LINC02607):​n.307+21298G>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 0.321 in 152,002 control chromosomes in the GnomAD database, including 8,800 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 0.32 (8800 hom., cov: 32)
• Consequence: LINC02607 ENST00000456933.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

Genes affected

LINC02607 (HGNC:54049): (long intergenic non-protein coding RNA 2607)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02607	ENST00000456933.1	n.307+21298G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48829 AN: 151886 Hom.: 8798 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.321 AC: 48842 AN: 152002 Hom.: 8800 Cov.: 32 AF XY: 0.317 AC XY: 23560 AN XY: 74294

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.302

Alfa AF: 0.289 Hom.: 3434

Bravo AF: 0.322

Asia WGS AF: 0.125 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1396626; hg19: chr1-96025546;