chr12-110224522-C-T

Variant names:

• chr12-110224522-C-T
• rs7304243
• ENST00000746208.1:n.1027-22533G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000746208.1(ENSG00000289311):​n.1027-22533G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,102 control chromosomes in the GnomAD database, including 41,369 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 0.73 (41369 hom., cov: 31)
• Consequence: ENSG00000289311 ENST00000746208.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772
• Publications: 11 publications found

Genes affected

ENSG00000289311 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289311	ENST00000746208.1	n.1027-22533G>A		intron_variant	Intron 1 of 3
ENSG00000289311	ENST00000746209.1	n.720-3648G>A		intron_variant	Intron 3 of 3
ENSG00000289311	ENST00000746210.1	n.215-3648G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111156 AN: 151984 Hom.: 41330 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.731 AC: 111251 AN: 152102 Hom.: 41369 Cov.: 31 AF XY: 0.725 AC XY: 53880 AN XY: 74338

African (AFR) AF: 0.860 AC: 35691 AN: 41508

American (AMR) AF: 0.688 AC: 10494 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2537 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3900 AN: 5170

South Asian (SAS) AF: 0.472 AC: 2272 AN: 4814

European-Finnish (FIN) AF: 0.678 AC: 7151 AN: 10554

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46803 AN: 68008

Other (OTH) AF: 0.726 AC: 1534 AN: 2112

Alfa AF: 0.702 Hom.: 63723

Bravo AF: 0.746

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs7304243; hg19: chr12-110662327;