chr12-12723177-C-G

Variant names:

• chr12-12723177-C-G
• rs1420023
• ENST00000726600.1:n.283+46G>C

Variant summary

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

The ENST00000726600.1(ENSG00000256658):​n.283+46G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 151,822 control chromosomes in the GnomAD database, including 688 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 0.086 (688 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000256658 ENST00000726600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45
• Publications: 17 publications found

Genes affected

ENSG00000256658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369663	XR_931366.4	n.1901+46G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256658	ENST00000726600.1	n.283+46G>C		intron_variant	Intron 2 of 2
ENSG00000256658	ENST00000542291.1	n.*120G>C		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13040 AN: 151710 Hom.: 688 Cov.: 32

Gnomad AFR AF: 0.0297

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0859 AC: 13035 AN: 151822 Hom.: 688 Cov.: 32 AF XY: 0.0868 AC XY: 6441 AN XY: 74198

African (AFR) AF: 0.0296 AC: 1223 AN: 41384

American (AMR) AF: 0.0768 AC: 1171 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3468

East Asian (EAS) AF: 0.132 AC: 686 AN: 5178

South Asian (SAS) AF: 0.140 AC: 674 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1115 AN: 10444

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7389 AN: 67976

Other (OTH) AF: 0.0904 AC: 190 AN: 2102

Alfa AF: 0.0400 Hom.: 30

Bravo AF: 0.0812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.0090
DANN	Benign	0.69
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1420023; hg19: chr12-12876111;