chr7-119765676-G-T

Variant names:

• chr7-119765676-G-T
• rs1404084
• ENST00000426413.2:n.239-13501C>A

Variant summary

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

The ENST00000426413.2(LINC02476):​n.239-13501C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 152,168 control chromosomes in the GnomAD database, including 66,537 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 (66537 hom., cov: 32)
• Consequence: LINC02476 ENST00000426413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02476	NR_131960.1		n.299+16608C>A		intron	N/A
	LINC02476	NR_131961.1		n.217-13501C>A		intron	N/A
	LINC02476	NR_131962.1		n.142+35140C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02476	ENST00000426413.2	TSL:2	n.239-13501C>A		intron	N/A
	LINC02476	ENST00000431071.5	TSL:4	n.142+35140C>A		intron	N/A
	LINC02476	ENST00000660268.1		n.216+16608C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141855 AN: 152050 Hom.: 66504 Cov.: 32

Gnomad AFR AF: 0.834

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: 0.933 AC: 141946 AN: 152168 Hom.: 66537 Cov.: 32 AF XY: 0.936 AC XY: 69628 AN XY: 74410

African (AFR) AF: 0.833 AC: 34564 AN: 41470

American (AMR) AF: 0.958 AC: 14637 AN: 15276

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

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5166

South Asian (SAS) AF: 0.979 AC: 4729 AN: 4830

European-Finnish (FIN) AF: 0.992 AC: 10537 AN: 10622

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

European-Non Finnish (NFE) AF: 0.968 AC: 65822 AN: 68014

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

Alfa AF: 0.943 Hom.: 8798

Bravo AF: 0.924

Asia WGS AF: 0.979 AC: 3404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.29
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1404084; hg19: chr7-119405730;