chr12-7182217-C-T

Variant names:

• chr12-7182217-C-T
• rs7973719
• ENST00000543061.1:n.324+6529G>A

Variant summary

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

The ENST00000543061.1(ENSG00000255572):​n.324+6529G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,972 control chromosomes in the GnomAD database, including 15,649 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 0.42 (15649 hom., cov: 31)
• Consequence: ENSG00000255572 ENST00000543061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 13 publications found

Genes affected

ENSG00000255572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543061.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255572	ENST00000543061.1	TSL:2	n.324+6529G>A		intron	N/A
	ENSG00000255572	ENST00000545794.1	TSL:3	n.279+6529G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64516 AN: 151854 Hom.: 15639 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.425 AC: 64528 AN: 151972 Hom.: 15649 Cov.: 31 AF XY: 0.425 AC XY: 31542 AN XY: 74254

African (AFR) AF: 0.187 AC: 7765 AN: 41468

American (AMR) AF: 0.598 AC: 9140 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1674 AN: 3464

East Asian (EAS) AF: 0.383 AC: 1970 AN: 5150

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4653 AN: 10530

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35370 AN: 67958

Other (OTH) AF: 0.465 AC: 977 AN: 2102

Alfa AF: 0.470 Hom.: 2198

Bravo AF: 0.427

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7973719; hg19: chr12-7334813;