rs2950354

Variant names:

• chr10-122888375-C-A
• rs2950354
• ENST00000368895.2:n.748C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-122888375-C-A
• chr10-122888375-C-T

Variant summary

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

The ENST00000425266.4(ENSG00000293310):​n.532C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 380,554 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: not found (cov: 32)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: ENSG00000293310 ENST00000425266.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 0 publications found

Genes affected

C10orf88B (HGNC:44080): (C10orf88B (pseudogene))

ENSG00000293310 (HGNC:):

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=-0.6).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425266.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	NR_027282.1		n.842C>A		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	ENST00000368895.2	TSL:6	n.748C>A		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000293310	ENST00000425266.4	TSL:2	n.532C>A		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000293310	ENST00000701528.1		n.290C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000105 AC: 4 AN: 380554 Hom.: 0 Cov.: 0 AF XY: 0.0000138 AC XY: 3 AN XY: 216772

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

African (AFR) AF: 0.00 AC: 0 AN: 10482

American (AMR) AF: 0.00 AC: 0 AN: 36226

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11738

East Asian (EAS) AF: 0.00 AC: 0 AN: 13142

South Asian (SAS) AF: 0.0000594 AC: 4 AN: 67366

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30104

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2854

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 191956

Other (OTH) AF: 0.00 AC: 0 AN: 16686

⚠️ 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 Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs2950354; hg19: chr10-124647891;