rs4461995

Positions:

• chr9-16366743-T-C

Variant summary

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

The ENST00000648575.1(LINC03041):​n.173+33677A>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 0.194 in 152,172 control chromosomes in the GnomAD database, including 3,601 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 0.19 (3601 hom., cov: 32)
• Consequence: LINC03041 ENST00000648575.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923

Genes affected

LINC03041 (HGNC:19054): (long intergenic non-protein coding RNA 3041)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03041	ENST00000648575.1	n.173+33677A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29540 AN: 152054 Hom.: 3597 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.194 AC: 29567 AN: 152172 Hom.: 3601 Cov.: 32 AF XY: 0.191 AC XY: 14236 AN XY: 74402

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.166

Alfa AF: 0.157 Hom.: 1091

Bravo AF: 0.202

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4461995; hg19: chr9-16366741;