rs9893303

Positions:

• chr17-72429677-T-C

Variant summary

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

The NR_152515.1(LINC00673):​n.603-1379A>G 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 0.164 in 152,212 control chromosomes in the GnomAD database, including 2,555 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 0.16 (2555 hom., cov: 32)
• Consequence: LINC00673 NR_152515.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

Genes affected

LINC00511 (HGNC:43564): (long intergenic non-protein coding RNA 511)

LINC00673 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00673	NR_152515.1	n.603-1379A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00511	ENST00000648631.1	n.700-1379A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24961 AN: 152094 Hom.: 2549 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.164 AC: 24999 AN: 152212 Hom.: 2555 Cov.: 32 AF XY: 0.161 AC XY: 12020 AN XY: 74428

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.152

Alfa AF: 0.133 Hom.: 1904

Bravo AF: 0.165

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9893303; hg19: chr17-70425818;