rs2505990

Variant names:

• chr10-43069900-C-A
• rs2505990
• ENST00000794440.1:n.257+1406G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-43069900-C-A
• chr10-43069900-C-G
• chr10-43069900-C-T

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.257+1406G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,096 control chromosomes in the GnomAD database, including 50,593 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 0.81 (50593 hom., cov: 32)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 1 publications found

Genes affected

ENSG00000303432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 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
ENSG00000303432	ENST00000794440.1	n.257+1406G>T		intron_variant	Intron 2 of 2
ENSG00000303432	ENST00000794441.1	n.322+1406G>T		intron_variant	Intron 2 of 3
ENSG00000303432	ENST00000794442.1	n.313+1406G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122893 AN: 151978 Hom.: 50526 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.809 AC: 123024 AN: 152096 Hom.: 50593 Cov.: 32 AF XY: 0.801 AC XY: 59567 AN XY: 74328

African (AFR) AF: 0.957 AC: 39749 AN: 41540

American (AMR) AF: 0.775 AC: 11849 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3569 AN: 5114

South Asian (SAS) AF: 0.742 AC: 3577 AN: 4822

European-Finnish (FIN) AF: 0.649 AC: 6856 AN: 10570

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52296 AN: 67974

Other (OTH) AF: 0.797 AC: 1681 AN: 2110

Alfa AF: 0.774 Hom.: 6722

Bravo AF: 0.828

Asia WGS AF: 0.732 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2505990; hg19: chr10-43565348;