chr12-5162958-A-C

Variant names:

• chr12-5162958-A-C
• rs11063543
• ENST00000789688.1:n.278-6849A>C

Variant summary

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

The ENST00000789688.1(ENSG00000256417):​n.278-6849A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,260 control chromosomes in the GnomAD database, including 2,062 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 0.16 (2062 hom., cov: 32)
• Consequence: ENSG00000256417 ENST00000789688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 4 publications found

Genes affected

ENSG00000256417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369617	NR_188065.1	n.617+2573A>C		intron_variant	Intron 2 of 10
LOC105369617	NR_188066.1	n.600+2573A>C		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256417	ENST00000789688.1	n.278-6849A>C		intron_variant	Intron 2 of 8
ENSG00000256417	ENST00000789689.1	n.348+2573A>C		intron_variant	Intron 3 of 11
ENSG00000256417	ENST00000789690.1	n.334+2573A>C		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24429 AN: 152142 Hom.: 2056 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.161 AC: 24458 AN: 152260 Hom.: 2062 Cov.: 32 AF XY: 0.159 AC XY: 11866 AN XY: 74456

African (AFR) AF: 0.180 AC: 7462 AN: 41534

American (AMR) AF: 0.147 AC: 2248 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3468

East Asian (EAS) AF: 0.168 AC: 869 AN: 5180

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4830

European-Finnish (FIN) AF: 0.182 AC: 1930 AN: 10604

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10606 AN: 68024

Other (OTH) AF: 0.150 AC: 318 AN: 2116

Alfa AF: 0.153 Hom.: 2231

Bravo AF: 0.158

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.63
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs11063543; hg19: chr12-5272124;