7-119823606-C-A

Variant names:

• chr7-119823606-C-A
• rs4730942
• ENST00000426413.2:n.106-22732G>T

Variant summary

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

The ENST00000426413.2(LINC02476):​n.106-22732G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,204 control chromosomes in the GnomAD database, including 66,409 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 0.93 (66409 hom., cov: 33)
• Consequence: LINC02476 ENST00000426413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 1 publications found

Genes affected

LINC02476 (HGNC:53419): (long intergenic non-protein coding RNA 2476)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02476	NR_131960.1	n.84-7026G>T		intron_variant	Intron 1 of 4
LINC02476	NR_131961.1	n.84-22732G>T		intron_variant	Intron 1 of 3
LINC02476	NR_131962.1	n.84-22732G>T		intron_variant	Intron 1 of 2
LINC02476	NR_131963.1	n.84-22732G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02476	ENST00000426413.2	n.106-22732G>T		intron_variant	Intron 1 of 3	2
LINC02476	ENST00000431071.5	n.84-22732G>T		intron_variant	Intron 1 of 2	4
LINC02476	ENST00000660268.1	n.84-22732G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141756 AN: 152086 Hom.: 66378 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.932 AC: 141845 AN: 152204 Hom.: 66409 Cov.: 33 AF XY: 0.935 AC XY: 69571 AN XY: 74430

African (AFR) AF: 0.830 AC: 34443 AN: 41482

American (AMR) AF: 0.958 AC: 14647 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3342 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5172

South Asian (SAS) AF: 0.978 AC: 4722 AN: 4826

European-Finnish (FIN) AF: 0.992 AC: 10532 AN: 10616

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65840 AN: 68030

Other (OTH) AF: 0.933 AC: 1970 AN: 2112

Alfa AF: 0.944 Hom.: 4106

Bravo AF: 0.923

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.40
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4730942; hg19: chr7-119463660;