rs10495712

Variant names:

• chr2-20973240-A-G
• rs10495712
• ENST00000764419.1:n.*212A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-20973240-A-G
• chr2-20973240-A-T

Variant summary

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

The ENST00000764419.1(ENSG00000299535):​n.*212A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,180 control chromosomes in the GnomAD database, including 45,792 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 0.77 (45792 hom., cov: 33)
• Consequence: ENSG00000299535 ENST00000764419.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 11 publications found

Genes affected

ENSG00000299535 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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
ENSG00000299535	ENST00000764419.1	n.*212A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117647 AN: 152062 Hom.: 45767 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.774 AC: 117722 AN: 152180 Hom.: 45792 Cov.: 33 AF XY: 0.774 AC XY: 57571 AN XY: 74398

African (AFR) AF: 0.823 AC: 34194 AN: 41534

American (AMR) AF: 0.730 AC: 11154 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2805 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4905 AN: 5182

South Asian (SAS) AF: 0.839 AC: 4043 AN: 4820

European-Finnish (FIN) AF: 0.744 AC: 7866 AN: 10568

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50166 AN: 68012

Other (OTH) AF: 0.813 AC: 1716 AN: 2110

Alfa AF: 0.753 Hom.: 73190

Bravo AF: 0.776

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.53
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10495712; hg19: chr2-21196112;