7-119853516-T-C

Position:

• chr7-119853516-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02476 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02476	NR_131960.1	n.84-36936A>G		intron_variant
LINC02476	NR_131961.1	n.84-52642A>G		intron_variant
LINC02476	NR_131962.1	n.84-52642A>G		intron_variant
LINC02476	NR_131963.1	n.84-52642A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02476	ENST00000426413.2	n.106-52642A>G		intron_variant		2
LINC02476	ENST00000431071.5	n.84-52642A>G		intron_variant		4
LINC02476	ENST00000660268.1	n.84-52642A>G		intron_variant

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

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.632

Alfa AF: 0.583 Hom.: 53196

Bravo AF: 0.658

Asia WGS AF: 0.514 AC: 1789 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs846427; hg19: chr7-119493570;