chr10-43076540-T-C

Variant names:

• chr10-43076540-T-C
• rs2435366
• ENST00000794440.1:n.51+521A>G

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.51+521A>G 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 152,194 control chromosomes in the GnomAD database, including 48,817 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 (48817 hom., cov: 35)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 2 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=-0.79).
• 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+521A>G		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.116+493A>G		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.107+493A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120446 AN: 152076 Hom.: 48750 Cov.: 35

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.754

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: 120580 AN: 152194 Hom.: 48817 Cov.: 35 AF XY: 0.785 AC XY: 58363 AN XY: 74382

African (AFR) AF: 0.953 AC: 39611 AN: 41578

American (AMR) AF: 0.766 AC: 11727 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2428 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2759 AN: 5118

South Asian (SAS) AF: 0.712 AC: 3430 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6780 AN: 10604

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.754 AC: 51229 AN: 67984

Other (OTH) AF: 0.778 AC: 1646 AN: 2116

Alfa AF: 0.767 Hom.: 5635

Bravo AF: 0.811

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs2435366; hg19: chr10-43571988;