ENST00000794440.1:n.52-79G>C

Variant names:

• chr10-43071590-C-G
• rs2505992
• ENST00000794440.1:n.52-79G>C

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.52-79G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,974 control chromosomes in the GnomAD database, including 21,660 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 0.53 (21660 hom., cov: 32)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 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.52-79G>C		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.117-79G>C		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.108-79G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80807 AN: 151856 Hom.: 21635 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.532 AC: 80885 AN: 151974 Hom.: 21660 Cov.: 32 AF XY: 0.531 AC XY: 39396 AN XY: 74250

African (AFR) AF: 0.547 AC: 22645 AN: 41436

American (AMR) AF: 0.525 AC: 8014 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3466

East Asian (EAS) AF: 0.434 AC: 2238 AN: 5162

South Asian (SAS) AF: 0.538 AC: 2583 AN: 4804

European-Finnish (FIN) AF: 0.505 AC: 5329 AN: 10546

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36746 AN: 67964

Other (OTH) AF: 0.493 AC: 1043 AN: 2114

Alfa AF: 0.520 Hom.: 2478

Bravo AF: 0.536

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.53
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2505992; hg19: chr10-43567038;