rs776207

Variant names:

• chr12-69631642-G-A
• rs776207
• ENST00000812541.1:n.286+6692G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-69631642-G-A
• chr12-69631642-G-C

Variant summary

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

The ENST00000812541.1(ENSG00000305711):​n.286+6692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,032 control chromosomes in the GnomAD database, including 33,058 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 0.64 (33058 hom., cov: 31)
• Consequence: ENSG00000305711 ENST00000812541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• 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 = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369823	XR_007063357.1	n.106+6692G>A		intron_variant	Intron 2 of 3
LOC105369823	XR_007063358.1	n.106+6692G>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+6692G>A		intron_variant	Intron 2 of 3
ENSG00000305711	ENST00000812542.1	n.365+6692G>A		intron_variant	Intron 2 of 4
ENSG00000305711	ENST00000812543.1	n.354+6692G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97342 AN: 151912 Hom.: 33008 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.641 AC: 97453 AN: 152032 Hom.: 33058 Cov.: 31 AF XY: 0.646 AC XY: 48008 AN XY: 74294

African (AFR) AF: 0.817 AC: 33898 AN: 41488

American (AMR) AF: 0.674 AC: 10297 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2011 AN: 3470

East Asian (EAS) AF: 0.984 AC: 5094 AN: 5178

South Asian (SAS) AF: 0.779 AC: 3757 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5670 AN: 10542

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34773 AN: 67940

Other (OTH) AF: 0.644 AC: 1356 AN: 2106

Alfa AF: 0.560 Hom.: 40464

Bravo AF: 0.662

Asia WGS AF: 0.861 AC: 2996 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	0.17
DANN	Benign	0.12
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs776207; hg19: chr12-70025422;