chr12-75687076-T-C

Variant names:

• chr12-75687076-T-C
• rs17223072
• ENST00000552856.1:n.401+5029A>G

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.401+5029A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 152,160 control chromosomes in the GnomAD database, including 689 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 0.091 (689 hom., cov: 31)
• Consequence: ENSG00000258077 ENST00000552856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 3 publications found

Genes affected

ENSG00000258077 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369844	XR_007063374.1	n.691+5029A>G		intron_variant	Intron 5 of 6
LOC105369844	XR_007063375.1	n.1371+5029A>G		intron_variant	Intron 6 of 15
LOC105369844	XR_007063376.1	n.2298+5029A>G		intron_variant	Intron 4 of 7
LOC105369844	XR_007063377.1	n.2298+5029A>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258077	ENST00000552856.1	n.401+5029A>G		intron_variant	Intron 3 of 4	3
ENSG00000286259	ENST00000651075.1	n.323-1652T>C		intron_variant	Intron 4 of 5
ENSG00000258077	ENST00000741371.1	n.527+5029A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13864 AN: 152042 Hom.: 688 Cov.: 31

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0912 AC: 13872 AN: 152160 Hom.: 689 Cov.: 31 AF XY: 0.0914 AC XY: 6797 AN XY: 74382

African (AFR) AF: 0.0367 AC: 1526 AN: 41544

American (AMR) AF: 0.111 AC: 1698 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.0836 AC: 433 AN: 5178

South Asian (SAS) AF: 0.0831 AC: 400 AN: 4814

European-Finnish (FIN) AF: 0.114 AC: 1210 AN: 10578

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7863 AN: 67990

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.106 Hom.: 171

Bravo AF: 0.0883

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.30
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: rs17223072; hg19: chr12-76080856;