10-43073439-T-C

Variant names:

• chr10-43073439-T-C
• rs2505994
• ENST00000794440.1:n.52-1928A>G

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.52-1928A>G 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 152,242 control chromosomes in the GnomAD database, including 50,675 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 (50675 hom., cov: 34)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 3 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 = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794440.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303432	ENST00000794440.1		n.52-1928A>G		intron	N/A
	ENSG00000303432	ENST00000794441.1		n.117-1928A>G		intron	N/A
	ENSG00000303432	ENST00000794442.1		n.108-1928A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123049 AN: 152124 Hom.: 50611 Cov.: 34

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.809 AC: 123176 AN: 152242 Hom.: 50675 Cov.: 34 AF XY: 0.802 AC XY: 59682 AN XY: 74422

African (AFR) AF: 0.956 AC: 39758 AN: 41568

American (AMR) AF: 0.772 AC: 11809 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2465 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3583 AN: 5168

South Asian (SAS) AF: 0.758 AC: 3666 AN: 4834

European-Finnish (FIN) AF: 0.651 AC: 6891 AN: 10592

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52354 AN: 67986

Other (OTH) AF: 0.792 AC: 1673 AN: 2112

Alfa AF: 0.788 Hom.: 7522

Bravo AF: 0.827

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.79
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2505994; hg19: chr10-43568887;