chr7-119765676-G-T

Position:

• chr7-119765676-G-T

Variant summary

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

The NR_131960.1(LINC02476):​n.299+16608C>A 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 0.933 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 NR_131960.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

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=-1.01).
• 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.299+16608C>A		intron_variant, non_coding_transcript_variant
LINC02476	NR_131961.1	n.217-13501C>A		intron_variant, non_coding_transcript_variant
LINC02476	NR_131962.1	n.142+35140C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02476	ENST00000660268.1	n.216+16608C>A		intron_variant, non_coding_transcript_variant
LINC02476	ENST00000426413.2	n.239-13501C>A		intron_variant, non_coding_transcript_variant		2
LINC02476	ENST00000431071.5	n.142+35140C>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.979

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.933

Alfa AF: 0.948 Hom.: 8524

Bravo AF: 0.924

Asia WGS AF: 0.979 AC: 3404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404084; hg19: chr7-119405730;