ENST00000412811.2:n.302-2533A>G

Variant names:

• chr3-40859859-A-G
• rs10510710
• ENST00000412811.2:n.302-2533A>G

Variant summary

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

The ENST00000412811.2(ENSG00000231873):​n.302-2533A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,272 control chromosomes in the GnomAD database, including 449 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 0.066 (449 hom., cov: 32)
• Consequence: ENSG00000231873 ENST00000412811.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 1 publications found

Genes affected

ENSG00000231873 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377043	XR_007095885.1	n.266-51089A>G		intron_variant	Intron 2 of 2
LOC105377043	XR_940766.3	n.266-10025A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231873	ENST00000412811.2	n.302-2533A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10008 AN: 152154 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0685

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0658 AC: 10021 AN: 152272 Hom.: 449 Cov.: 32 AF XY: 0.0634 AC XY: 4723 AN XY: 74464

African (AFR) AF: 0.130 AC: 5405 AN: 41538

American (AMR) AF: 0.0685 AC: 1048 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3470

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5182

South Asian (SAS) AF: 0.0122 AC: 59 AN: 4822

European-Finnish (FIN) AF: 0.0161 AC: 171 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0426 AC: 2900 AN: 68028

Other (OTH) AF: 0.0616 AC: 130 AN: 2110

Alfa AF: 0.0698 Hom.: 291

Bravo AF: 0.0731

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.58
DANN	Benign	0.69
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10510710; hg19: chr3-40901350;