rs495795

Variant names:

• chr22-12200388-G-A
• rs495795
• ENST00000754819.1:n.371-18758G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-12200388-G-A
• chr22-12200388-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000754819.1(ENSG00000298316):​n.371-18758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.020 (0 hom., cov: 74)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000298316 ENST00000754819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 publications found

Genes affected

ENSG00000298316 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=6.708).

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
ENSG00000298316	ENST00000754819.1	n.371-18758G>A		intron_variant	Intron 3 of 3
ENSG00000298316	ENST00000754820.1	n.578-5417G>A		intron_variant	Intron 4 of 6
ENSG00000298316	ENST00000754821.1	n.403-18758G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2351 AN: 120128 Hom.: 0 Cov.: 74

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0125

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.0273

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.0297

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0536

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0203

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0195 AC: 2348 AN: 120234 Hom.: 0 Cov.: 74 AF XY: 0.0203 AC XY: 1196 AN XY: 58908

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

African (AFR) AF: 0.0128 AC: 441 AN: 34570

American (AMR) AF: 0.0226 AC: 261 AN: 11574

Ashkenazi Jewish (ASJ) AF: 0.0273 AC: 69 AN: 2532

East Asian (EAS) AF: 0.0637 AC: 228 AN: 3580

South Asian (SAS) AF: 0.0292 AC: 108 AN: 3696

European-Finnish (FIN) AF: 0.0201 AC: 163 AN: 8120

Middle Eastern (MID) AF: 0.0476 AC: 10 AN: 210

European-Non Finnish (NFE) AF: 0.0191 AC: 1025 AN: 53594

Other (OTH) AF: 0.0208 AC: 34 AN: 1638

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0524 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.7
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs495795; hg19: -;