chr12-96464584-A-T

Variant names:

• chr12-96464584-A-T
• rs12423247
• ENST00000548740.1:n.226+18866T>A

Variant summary

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

The ENST00000548740.1(ENSG00000258272):​n.226+18866T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0908 in 152,182 control chromosomes in the GnomAD database, including 1,263 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 (1263 hom., cov: 31)
• Consequence: ENSG00000258272 ENST00000548740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 10 publications found

Genes affected

ENSG00000258272 (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 (AFR) allele frequency at 95% confidence interval = 0.226 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
ENSG00000258272	ENST00000548740.1	n.226+18866T>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13765 AN: 152064 Hom.: 1255 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.0908 AC: 13818 AN: 152182 Hom.: 1263 Cov.: 31 AF XY: 0.0903 AC XY: 6721 AN XY: 74408

African (AFR) AF: 0.230 AC: 9537 AN: 41500

American (AMR) AF: 0.0865 AC: 1321 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.105 AC: 544 AN: 5186

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4828

European-Finnish (FIN) AF: 0.0210 AC: 222 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1487 AN: 68012

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0389 Hom.: 168

Bravo AF: 0.102

Asia WGS AF: 0.113 AC: 392 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	2.0
DANN	Benign	0.54
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12423247; hg19: chr12-96858362;