chr12-10023545-C-T

Variant names:

• chr12-10023545-C-T
• rs10505745
• ENST00000544225.2:n.300+4370G>A

Variant summary

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

The ENST00000544225.2(ENSG00000256803):​n.300+4370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,132 control chromosomes in the GnomAD database, including 1,944 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 0.15 (1944 hom., cov: 32)
• Consequence: ENSG00000256803 ENST00000544225.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 4 publications found

Genes affected

ENSG00000256803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724020	NR_120484.1	n.248+4370G>A		intron_variant	Intron 2 of 2
LOC102724020	NR_169587.1	n.257+4254G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256803	ENST00000544225.2	n.300+4370G>A		intron_variant	Intron 2 of 2	3
ENSG00000256803	ENST00000787688.1	n.280+4370G>A		intron_variant	Intron 2 of 3
ENSG00000256803	ENST00000787689.1	n.287+4254G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22579 AN: 152014 Hom.: 1946 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.148 AC: 22581 AN: 152132 Hom.: 1944 Cov.: 32 AF XY: 0.145 AC XY: 10791 AN XY: 74352

African (AFR) AF: 0.0849 AC: 3523 AN: 41516

American (AMR) AF: 0.123 AC: 1885 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.166 AC: 860 AN: 5178

South Asian (SAS) AF: 0.126 AC: 609 AN: 4816

European-Finnish (FIN) AF: 0.122 AC: 1292 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13172 AN: 67970

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.179 Hom.: 10740

Bravo AF: 0.148

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.55
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10505745; hg19: chr12-10176144;