1-95568926-C-T

Variant names:

• chr1-95568926-C-T
• rs6593669
• ENST00000456933.1:n.307+30234C>T

Variant summary

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

The ENST00000456933.1(LINC02607):​n.307+30234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 151,960 control chromosomes in the GnomAD database, including 41,211 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 0.73 (41211 hom., cov: 32)
• Consequence: LINC02607 ENST00000456933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456933.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02607	ENST00000456933.1	TSL:3	n.307+30234C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110299 AN: 151842 Hom.: 41217 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.726 AC: 110311 AN: 151960 Hom.: 41211 Cov.: 32 AF XY: 0.720 AC XY: 53504 AN XY: 74282

African (AFR) AF: 0.565 AC: 23381 AN: 41392

American (AMR) AF: 0.733 AC: 11197 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2717 AN: 3466

East Asian (EAS) AF: 0.508 AC: 2618 AN: 5154

South Asian (SAS) AF: 0.618 AC: 2974 AN: 4814

European-Finnish (FIN) AF: 0.804 AC: 8493 AN: 10562

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56370 AN: 67988

Other (OTH) AF: 0.748 AC: 1579 AN: 2110

Alfa AF: 0.791 Hom.: 138511

Bravo AF: 0.719

Asia WGS AF: 0.525 AC: 1827 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6593669; hg19: chr1-96034482;