chr5-42175050-A-C

Variant names:

• chr5-42175050-A-C
• rs1501516
• ENST00000790879.1:n.255+10798T>G

Variant summary

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

The ENST00000790879.1(LINC02996):​n.255+10798T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,138 control chromosomes in the GnomAD database, including 34,883 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 0.67 (34883 hom., cov: 33)
• Consequence: LINC02996 ENST00000790879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 3 publications found

Genes affected

LINC02996 (HGNC:):

LINC02996 (HGNC:56112): (long intergenic non-protein coding RNA 2996)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02996	NR_104635.1	n.193+103T>G		intron_variant	Intron 1 of 3
LINC02996	NR_104636.1	n.193+103T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02996	ENST00000790879.1	n.255+10798T>G		intron_variant	Intron 2 of 4
LINC02996	ENST00000790880.1	n.362+103T>G		intron_variant	Intron 3 of 4
LINC02996	ENST00000790881.1	n.208+10798T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102195 AN: 152020 Hom.: 34849 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.672 AC: 102283 AN: 152138 Hom.: 34883 Cov.: 33 AF XY: 0.675 AC XY: 50229 AN XY: 74384

African (AFR) AF: 0.610 AC: 25323 AN: 41480

American (AMR) AF: 0.717 AC: 10952 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2297 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5168 AN: 5182

South Asian (SAS) AF: 0.771 AC: 3725 AN: 4830

European-Finnish (FIN) AF: 0.674 AC: 7131 AN: 10586

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45624 AN: 68000

Other (OTH) AF: 0.654 AC: 1382 AN: 2114

Alfa AF: 0.664 Hom.: 5503

Bravo AF: 0.673

Asia WGS AF: 0.874 AC: 3037 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.75
DANN	Benign	0.60
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1501516; hg19: chr5-42175152;