12-131522286-T-G

Variant names:

• chr12-131522286-T-G
• rs10773917
• ENST00000653719.2:n.206+7405A>C

Variant summary

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

The ENST00000653719.2(ENSG00000256209):​n.206+7405A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 121,504 control chromosomes in the GnomAD database, including 31,578 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 0.71 (31578 hom., cov: 29)
• Consequence: ENSG00000256209 ENST00000653719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05
• Publications: 1 publications found

Genes affected

ENSG00000256209 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929974	NR_187799.1	n.100+7489A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256209	ENST00000653719.2	n.206+7405A>C		intron_variant	Intron 1 of 3
ENSG00000256209	ENST00000658806.2	n.145+7489A>C		intron_variant	Intron 1 of 3
ENSG00000256209	ENST00000833612.1	n.152+7489A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.715 AC: 86803 AN: 121454 Hom.: 31566 Cov.: 29

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.715 AC: 86837 AN: 121504 Hom.: 31578 Cov.: 29 AF XY: 0.716 AC XY: 43103 AN XY: 60202

African (AFR) AF: 0.585 AC: 15300 AN: 26176

American (AMR) AF: 0.741 AC: 9807 AN: 13242

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 1969 AN: 3012

East Asian (EAS) AF: 0.587 AC: 3022 AN: 5150

South Asian (SAS) AF: 0.568 AC: 2371 AN: 4176

European-Finnish (FIN) AF: 0.868 AC: 7867 AN: 9064

Middle Eastern (MID) AF: 0.687 AC: 169 AN: 246

European-Non Finnish (NFE) AF: 0.769 AC: 44453 AN: 57776

Other (OTH) AF: 0.670 AC: 1192 AN: 1780

Alfa AF: 0.774 Hom.: 54350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.18
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs10773917; hg19: chr12-132006831;