rs9701099

Variant names:

• chr1-630833-C-T
• rs9701099
• ENST00000452176.2:n.20+298G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000452176.2(ENSG00000293331):​n.20+298G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000076 in 131,524 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000076 (0 hom., cov: 26)
  • Exomes 𝑓: 0.0000042 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000293331 ENST00000452176.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

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+298G>A		intron_variant	Intron 1 of 3	1
LINC00115	ENST00000419394.2	n.481-43878G>A		intron_variant	Intron 3 of 3	5
ENSG00000293331	ENST00000440196.3	n.87-1827G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.00000760 AC: 1 AN: 131524 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.0000346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000425 AC: 1 AN: 235446 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 119596

African (AFR) AF: 0.00 AC: 0 AN: 5518

American (AMR) AF: 0.00 AC: 0 AN: 7106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8758

East Asian (EAS) AF: 0.0000496 AC: 1 AN: 20146

South Asian (SAS) AF: 0.00 AC: 0 AN: 2302

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22796

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

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 152226

Other (OTH) AF: 0.00 AC: 0 AN: 15442

GnomAD4 genome AF: 0.00000760 AC: 1 AN: 131524 Hom.: 0 Cov.: 26 AF XY: 0.0000156 AC XY: 1 AN XY: 63912

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

African (AFR) AF: 0.0000346 AC: 1 AN: 28912

American (AMR) AF: 0.00 AC: 0 AN: 13728

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3268

East Asian (EAS) AF: 0.00 AC: 0 AN: 4662

South Asian (SAS) AF: 0.00 AC: 0 AN: 3912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9444

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64666

Other (OTH) AF: 0.00 AC: 0 AN: 1828

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs9701099; hg19: chr1-566213;