chr18-42479656-G-T

Variant names:

• chr18-42479656-G-T
• rs16976171
• ENST00000585627.5:n.489+24667G>T

Variant summary

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

The ENST00000585627.5(LINC00907):​n.489+24667G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 151,480 control chromosomes in the GnomAD database, including 358 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 0.052 (358 hom., cov: 32)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.872+24667G>T		intron_variant	Intron 6 of 9
LINC00907	NR_046454.1	n.652+24667G>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.489+24667G>T		intron_variant	Intron 4 of 4	1
LINC00907	ENST00000585639.5	n.631+24667G>T		intron_variant	Intron 5 of 6	1
LINC00907	ENST00000591381.5	n.472+24667G>T		intron_variant	Intron 4 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7825 AN: 151378 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0395

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

GnomAD4 genome AF: 0.0517 AC: 7838 AN: 151480 Hom.: 358 Cov.: 32 AF XY: 0.0527 AC XY: 3901 AN XY: 73972

African (AFR) AF: 0.118 AC: 4865 AN: 41242

American (AMR) AF: 0.0406 AC: 618 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 106 AN: 3464

East Asian (EAS) AF: 0.0814 AC: 418 AN: 5138

South Asian (SAS) AF: 0.108 AC: 517 AN: 4790

European-Finnish (FIN) AF: 0.0143 AC: 149 AN: 10416

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.0157 AC: 1065 AN: 67930

Other (OTH) AF: 0.0430 AC: 90 AN: 2094

Alfa AF: 0.0252 Hom.: 120

Bravo AF: 0.0564

Asia WGS AF: 0.113 AC: 392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.21
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16976171; hg19: chr18-40059621;