chr4-187604743-T-C

Variant names:

• chr4-187604743-T-C
• rs952178
• ENST00000507817.3:n.271+61019A>G

Variant summary

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

The ENST00000507817.3(LINC02492):​n.271+61019A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 150,786 control chromosomes in the GnomAD database, including 35,523 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 0.69 (35523 hom., cov: 29)
• Consequence: LINC02492 ENST00000507817.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 3 publications found

Genes affected

LINC02492 (HGNC:53476): (long intergenic non-protein coding RNA 2492)

LOC105377604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02492	NR_110436.1	n.157+61019A>G		intron_variant	Intron 2 of 2
LOC105377604	XR_939612.3	n.156-11816A>G		intron_variant	Intron 1 of 3
LOC105377604	XR_939613.3	n.156-11816A>G		intron_variant	Intron 1 of 3
LOC105377604	XR_939614.3	n.156-11816A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02492	ENST00000507817.3	n.271+61019A>G		intron_variant	Intron 2 of 2	2
LINC02492	ENST00000514767.2	n.161+41467A>G		intron_variant	Intron 1 of 3	3
LINC02492	ENST00000515660.6	n.159-22213A>G		intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103212 AN: 150676 Hom.: 35499 Cov.: 29

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.685 AC: 103289 AN: 150786 Hom.: 35523 Cov.: 29 AF XY: 0.686 AC XY: 50478 AN XY: 73540

African (AFR) AF: 0.671 AC: 27642 AN: 41188

American (AMR) AF: 0.646 AC: 9699 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2410 AN: 3464

East Asian (EAS) AF: 0.978 AC: 5026 AN: 5140

South Asian (SAS) AF: 0.786 AC: 3757 AN: 4778

European-Finnish (FIN) AF: 0.644 AC: 6538 AN: 10160

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 45894 AN: 67758

Other (OTH) AF: 0.700 AC: 1466 AN: 2094

Alfa AF: 0.658 Hom.: 5352

Bravo AF: 0.684

Asia WGS AF: 0.863 AC: 2998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs952178; hg19: chr4-188525897;