rs6503919

chr17-59468604-A-G

Variant summary

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

The NR_110813.1(LINC01476):n.494+34375T>C 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 0.285 in 152,004 control chromosomes in the GnomAD database, including 7,989 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 0.28 (7989 hom., cov: 32)
• Consequence: LINC01476 NR_110813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

Genes affected

LINC01476 (HGNC:51117): (long intergenic non-protein coding RNA 1476)

LOC124904040 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01476	NR_110813.1	n.494+34375T>C		intron_variant, non_coding_transcript_variant
LOC124904040	XR_007065867.1	n.628+26968A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01476	ENST00000665301.2	n.488+34375T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43215 AN: 151886 Hom.: 7953 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.285 AC: 43291 AN: 152004 Hom.: 7989 Cov.: 32 AF XY: 0.285 AC XY: 21197 AN XY: 74294

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.295

Alfa AF: 0.187 Hom.: 6065

Bravo AF: 0.302

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.29
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: rs6503919; hg19: chr17-57545965;