rs9783068

Variant names:

• chr1-630825-T-C
• rs9783068
• ENST00000452176.2:n.20+306A>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The ENST00000452176.2(ENSG00000293331):​n.20+306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000412 in 130,916 control chromosomes in the GnomAD database, including 8 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 0.00041 (8 hom., cov: 26)
  • Exomes 𝑓: 0.000059 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000293331 ENST00000452176.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.725
• Publications: 1 publications found

Genes affected

ENSG00000293331 (HGNC:):

LINC00115 (HGNC:26211): (long intergenic non-protein coding RNA 115)

MTCO1P12 (HGNC:52014): (MT-CO1 pseudogene 12)

MTND2P28 (HGNC:42129): (MT-ND2 pseudogene 28)

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BS2: High Homozygotes in GnomAd4 at 8 gene

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
ENSG00000293331	ENST00000452176.2	n.20+306A>G		intron_variant	Intron 1 of 3	1
LINC00115	ENST00000419394.2	n.481-43870A>G		intron_variant	Intron 3 of 3	5
ENSG00000293331	ENST00000440196.3	n.87-1819A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.000413 AC: 54 AN: 130868 Hom.: 8 Cov.: 26

Gnomad AFR AF: 0.00148

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000659

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000464

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000595 AC: 14 AN: 235428 Hom.: 2 AF XY: 0.0000920 AC XY: 11 AN XY: 119618

African (AFR) AF: 0.00146 AC: 8 AN: 5490

American (AMR) AF: 0.00 AC: 0 AN: 7104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8754

East Asian (EAS) AF: 0.00 AC: 0 AN: 20132

South Asian (SAS) AF: 0.00 AC: 0 AN: 2338

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22824

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1152

European-Non Finnish (NFE) AF: 0.0000329 AC: 5 AN: 152196

Other (OTH) AF: 0.0000648 AC: 1 AN: 15438

GnomAD4 genome AF: 0.000412 AC: 54 AN: 130916 Hom.: 8 Cov.: 26 AF XY: 0.000487 AC XY: 31 AN XY: 63638

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

African (AFR) AF: 0.00148 AC: 42 AN: 28400

American (AMR) AF: 0.000658 AC: 9 AN: 13678

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3264

East Asian (EAS) AF: 0.00 AC: 0 AN: 4642

South Asian (SAS) AF: 0.00 AC: 0 AN: 3908

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 248

European-Non Finnish (NFE) AF: 0.0000464 AC: 3 AN: 64694

Other (OTH) AF: 0.00 AC: 0 AN: 1832

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000000000181302), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00523 Hom.: 10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	8.2
DANN	Benign	0.70
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs9783068; hg19: chr1-566205;