chr9-16366743-T-C

Variant names:

• chr9-16366743-T-C
• rs4461995
• ENST00000648575.1:n.173+33677A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648575.1(LINC03041):​n.173+33677A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03041	ENST00000648575.1	n.173+33677A>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.336 AC: 13941 AN: 41476

American (AMR) AF: 0.149 AC: 2278 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.126 AC: 608 AN: 4820

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10612

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10061 AN: 67998

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.159 Hom.: 1230

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
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs4461995; hg19: chr9-16366741;