ENST00000589068.5:n.1236+36415T>C

Variant names:

• chr18-42611606-T-C
• rs16976358
• ENST00000589068.5:n.1236+36415T>C

Variant summary

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

The ENST00000589068.5(LINC00907):​n.1236+36415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 152,286 control chromosomes in the GnomAD database, including 123 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 0.013 (123 hom., cov: 32)
• Consequence: LINC00907 ENST00000589068.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997
• Publications: 10 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.1271+36415T>C		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000589068.5	n.1236+36415T>C		intron_variant	Intron 7 of 9	2
LINC00907	ENST00000753323.1	n.557-31313T>C		intron_variant	Intron 5 of 5
LINC00907	ENST00000753324.1	n.992-31313T>C		intron_variant	Intron 6 of 7
LINC00907	ENST00000753335.1	n.451-31313T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0128 AC: 1942 AN: 152168 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.00299

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00491

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00613

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0129 AC: 1966 AN: 152286 Hom.: 123 Cov.: 32 AF XY: 0.0143 AC XY: 1066 AN XY: 74464

African (AFR) AF: 0.00306 AC: 127 AN: 41564

American (AMR) AF: 0.00490 AC: 75 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.186 AC: 960 AN: 5168

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4824

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00611 AC: 416 AN: 68030

Other (OTH) AF: 0.0213 AC: 45 AN: 2114

Alfa AF: 0.00673 Hom.: 6

Bravo AF: 0.0122

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.74
PhyloP100		1.0
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16976358; hg19: chr18-40191571;