3-41082244-C-T

Variant names:

• chr3-41082244-C-T
• rs10490823
• ENST00000808368.1:n.940-2053G>A

Variant summary

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

The ENST00000808368.1(ENSG00000305067):​n.940-2053G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,048 control chromosomes in the GnomAD database, including 14,830 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 0.41 (14830 hom., cov: 32)
• Consequence: ENSG00000305067 ENST00000808368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 20 publications found

Genes affected

ENSG00000305067 (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 (NFE) allele frequency at 95% confidence interval = 0.542 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
ENSG00000305067	ENST00000808368.1	n.940-2053G>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61635 AN: 151930 Hom.: 14827 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.405 AC: 61643 AN: 152048 Hom.: 14830 Cov.: 32 AF XY: 0.400 AC XY: 29718 AN XY: 74326

African (AFR) AF: 0.162 AC: 6730 AN: 41494

American (AMR) AF: 0.406 AC: 6190 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1253 AN: 5174

South Asian (SAS) AF: 0.275 AC: 1323 AN: 4808

European-Finnish (FIN) AF: 0.579 AC: 6113 AN: 10564

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37146 AN: 67962

Other (OTH) AF: 0.424 AC: 893 AN: 2108

Alfa AF: 0.491 Hom.: 84237

Bravo AF: 0.384

Asia WGS AF: 0.276 AC: 962 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	7.3
DANN	Benign	0.67
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10490823; hg19: chr3-41123735;