chr7-119823606-C-A

Position:

• chr7-119823606-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_131960.1(LINC02476):​n.84-7026G>T variant causes a intron, non coding transcript 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 NR_131960.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02476	NR_131960.1	n.84-7026G>T		intron_variant, non_coding_transcript_variant
LINC02476	NR_131961.1	n.84-22732G>T		intron_variant, non_coding_transcript_variant
LINC02476	NR_131962.1	n.84-22732G>T		intron_variant, non_coding_transcript_variant
LINC02476	NR_131963.1	n.84-22732G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02476	ENST00000660268.1	n.84-22732G>T		intron_variant, non_coding_transcript_variant
LINC02476	ENST00000426413.2	n.106-22732G>T		intron_variant, non_coding_transcript_variant		2
LINC02476	ENST00000431071.5	n.84-22732G>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.933

Alfa AF: 0.956 Hom.: 3840

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4730942; hg19: chr7-119463660;