ENST00000642091.1:n.44+15G>A

Variant names:

• chr6-29212944-G-A
• rs9257616
• ENST00000642091.1:n.44+15G>A

Variant summary

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

The ENST00000642091.1(ENSG00000290478):​n.44+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,044 control chromosomes in the GnomAD database, including 11,496 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 0.35 (11496 hom., cov: 31)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENSG00000290478 ENST00000642091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 19 publications found

Genes affected

ENSG00000290478 (HGNC:):

LINC03003 (HGNC:56126): (long intergenic non-protein coding RNA 3003)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 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
ENSG00000290478	ENST00000642091.1	n.44+15G>A		intron_variant	Intron 1 of 1
LINC03003	ENST00000733084.1	n.225+17362G>A		intron_variant	Intron 1 of 1
LINC03003	ENST00000733087.1	n.167+17362G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52978 AN: 151920 Hom.: 11481 Cov.: 31

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.339

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.349 AC: 52992 AN: 152038 Hom.: 11496 Cov.: 31 AF XY: 0.354 AC XY: 26274 AN XY: 74296

African (AFR) AF: 0.0851 AC: 3532 AN: 41502

American (AMR) AF: 0.405 AC: 6163 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1774 AN: 5170

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4824

European-Finnish (FIN) AF: 0.545 AC: 5745 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31487 AN: 67986

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.381 Hom.: 14846

Bravo AF: 0.322

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9257616; hg19: chr6-29180721;