rs2505998

Variant names:

• chr10-43075477-A-G
• rs2505998
• ENST00000794440.1:n.51+1584T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-43075477-A-G
• chr10-43075477-A-T

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.51+1584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,150 control chromosomes in the GnomAD database, including 48,774 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 0.79 (48774 hom., cov: 33)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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.51+1584T>C		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.116+1556T>C		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.107+1556T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120360 AN: 152032 Hom.: 48707 Cov.: 33

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.792 AC: 120494 AN: 152150 Hom.: 48774 Cov.: 33 AF XY: 0.784 AC XY: 58308 AN XY: 74348

African (AFR) AF: 0.953 AC: 39573 AN: 41538

American (AMR) AF: 0.766 AC: 11732 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2761 AN: 5150

South Asian (SAS) AF: 0.710 AC: 3426 AN: 4822

European-Finnish (FIN) AF: 0.640 AC: 6769 AN: 10582

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51190 AN: 67962

Other (OTH) AF: 0.778 AC: 1644 AN: 2112

Alfa AF: 0.755 Hom.: 13625

Bravo AF: 0.811

Asia WGS AF: 0.650 AC: 2263 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	0.33
DANN	Benign	0.47
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2505998; hg19: chr10-43570925;