7-119853516-T-C

Variant names:

• chr7-119853516-T-C
• rs846427
• ENST00000426413.2:n.106-52642A>G

Variant summary

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

The ENST00000426413.2(LINC02476):​n.106-52642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,922 control chromosomes in the GnomAD database, including 34,565 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 0.65 (34565 hom., cov: 32)
• Consequence: LINC02476 ENST00000426413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426413.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02476	NR_131960.1		n.84-36936A>G		intron	N/A
	LINC02476	NR_131961.1		n.84-52642A>G		intron	N/A
	LINC02476	NR_131962.1		n.84-52642A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02476	ENST00000426413.2	TSL:2	n.106-52642A>G		intron	N/A
	LINC02476	ENST00000431071.5	TSL:4	n.84-52642A>G		intron	N/A
	LINC02476	ENST00000660268.1		n.84-52642A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99031 AN: 151804 Hom.: 34504 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.653 AC: 99151 AN: 151922 Hom.: 34565 Cov.: 32 AF XY: 0.643 AC XY: 47784 AN XY: 74258

African (AFR) AF: 0.909 AC: 37709 AN: 41498

American (AMR) AF: 0.486 AC: 7411 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1931 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2743 AN: 5168

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4824

European-Finnish (FIN) AF: 0.597 AC: 6302 AN: 10552

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.580 AC: 39377 AN: 67846

Other (OTH) AF: 0.632 AC: 1328 AN: 2100

Alfa AF: 0.601 Hom.: 93066

Bravo AF: 0.658

Asia WGS AF: 0.514 AC: 1789 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.31
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs846427; hg19: chr7-119493570;