chr18-42525692-T-C

Variant names:

• chr18-42525692-T-C
• rs7231412
• ENST00000585639.5:n.683-7427T>C

Variant summary

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

The ENST00000585639.5(LINC00907):​n.683-7427T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,042 control chromosomes in the GnomAD database, including 3,701 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 0.20 (3701 hom., cov: 32)
• Consequence: LINC00907 ENST00000585639.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 8 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585639.5. 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
	LINC00907	NR_046174.2		n.873-49101T>C		intron	N/A
	LINC00907	NR_046454.1		n.704-7427T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	ENST00000585639.5	TSL:1	n.683-7427T>C		intron	N/A
	LINC00907	ENST00000589068.5	TSL:2	n.838-49101T>C		intron	N/A
	LINC00907	ENST00000753323.1		n.556+70703T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30648 AN: 151922 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.0982

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30686 AN: 152042 Hom.: 3701 Cov.: 32 AF XY: 0.201 AC XY: 14942 AN XY: 74316

African (AFR) AF: 0.299 AC: 12401 AN: 41468

American (AMR) AF: 0.246 AC: 3756 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3466

East Asian (EAS) AF: 0.445 AC: 2290 AN: 5144

South Asian (SAS) AF: 0.0980 AC: 472 AN: 4814

European-Finnish (FIN) AF: 0.115 AC: 1219 AN: 10600

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9347 AN: 67980

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.166 Hom.: 7930

Bravo AF: 0.221

Asia WGS AF: 0.291 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7231412;

hg19: chr18-40105657;