chr12-100181995-A-C

Variant names:

• chr12-100181995-A-C
• rs7960152
• ENST00000548404.7:n.803-1279T>G

Variant summary

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

The ENST00000548404.7(ENSG00000290576):​n.803-1279T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,110 control chromosomes in the GnomAD database, including 54,538 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 0.84 (54538 hom., cov: 31)
• Consequence: ENSG00000290576 ENST00000548404.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 5 publications found

Genes affected

ENSG00000290576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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
ENSG00000290576	ENST00000548404.7	n.803-1279T>G		intron_variant	Intron 4 of 12	3
ENSG00000257489	ENST00000548782.1	n.244-1279T>G		intron_variant	Intron 1 of 1	6
ENSG00000290576	ENST00000550096.5	n.394-1279T>G		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127935 AN: 151992 Hom.: 54484 Cov.: 31

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.842 AC: 128047 AN: 152110 Hom.: 54538 Cov.: 31 AF XY: 0.843 AC XY: 62680 AN XY: 74360

African (AFR) AF: 0.961 AC: 39895 AN: 41518

American (AMR) AF: 0.869 AC: 13267 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5157 AN: 5172

South Asian (SAS) AF: 0.897 AC: 4324 AN: 4822

European-Finnish (FIN) AF: 0.739 AC: 7788 AN: 10544

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52162 AN: 67998

Other (OTH) AF: 0.830 AC: 1749 AN: 2108

Alfa AF: 0.795 Hom.: 89721

Bravo AF: 0.857

Asia WGS AF: 0.929 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7960152; hg19: chr12-100575773;