rs295813

Variant names:

• chr2-156907351-A-G
• rs295813
• ENST00000762467.1:n.194+20789A>G

Variant summary

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

The ENST00000762467.1(ENSG00000287048):​n.194+20789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 150,938 control chromosomes in the GnomAD database, including 43,179 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 0.73 (43179 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000762467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 3 publications found

Genes affected

ENSG00000287048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 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
ENSG00000287048	ENST00000762467.1	n.194+20789A>G		intron_variant	Intron 2 of 2
ENSG00000287048	ENST00000762468.1	n.242+20789A>G		intron_variant	Intron 3 of 3
ENSG00000287048	ENST00000762469.1	n.362+20789A>G		intron_variant	Intron 4 of 4
ENSG00000287048	ENST00000762470.1	n.263+20789A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.729 AC: 109874 AN: 150820 Hom.: 43157 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.728 AC: 109931 AN: 150938 Hom.: 43179 Cov.: 32 AF XY: 0.729 AC XY: 53757 AN XY: 73752

African (AFR) AF: 0.408 AC: 16891 AN: 41364

American (AMR) AF: 0.758 AC: 11437 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3032 AN: 3448

East Asian (EAS) AF: 0.843 AC: 4316 AN: 5120

South Asian (SAS) AF: 0.807 AC: 3890 AN: 4822

European-Finnish (FIN) AF: 0.833 AC: 8799 AN: 10558

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.877 AC: 58984 AN: 67232

Other (OTH) AF: 0.740 AC: 1550 AN: 2094

Alfa AF: 0.799 Hom.: 6314

Bravo AF: 0.709

Asia WGS AF: 0.781 AC: 2682 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.51
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs295813; hg19: chr2-157763863;