ENST00000812541.1:n.286+4656G>A

Variant names:

• chr12-69629606-G-A
• rs776421
• ENST00000812541.1:n.286+4656G>A

Variant summary

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

The ENST00000812541.1(ENSG00000305711):​n.286+4656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,004 control chromosomes in the GnomAD database, including 27,931 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 0.59 (27931 hom., cov: 32)
• Consequence: ENSG00000305711 ENST00000812541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 4 publications found

Genes affected

ENSG00000305711 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369823	XR_007063357.1	n.106+4656G>A		intron_variant	Intron 2 of 3
LOC105369823	XR_007063358.1	n.106+4656G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305711	ENST00000812541.1	n.286+4656G>A		intron_variant	Intron 2 of 3
ENSG00000305711	ENST00000812542.1	n.365+4656G>A		intron_variant	Intron 2 of 4
ENSG00000305711	ENST00000812543.1	n.354+4656G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89771 AN: 151886 Hom.: 27890 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.591 AC: 89871 AN: 152004 Hom.: 27931 Cov.: 32 AF XY: 0.599 AC XY: 44523 AN XY: 74282

African (AFR) AF: 0.713 AC: 29575 AN: 41474

American (AMR) AF: 0.643 AC: 9830 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1880 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5081 AN: 5172

South Asian (SAS) AF: 0.735 AC: 3538 AN: 4814

European-Finnish (FIN) AF: 0.532 AC: 5600 AN: 10528

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32549 AN: 67958

Other (OTH) AF: 0.603 AC: 1273 AN: 2110

Alfa AF: 0.518 Hom.: 15565

Bravo AF: 0.608

Asia WGS AF: 0.840 AC: 2923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.72
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs776421; hg19: chr12-70023386;