chr12-93247422-T-C

Variant names:

• chr12-93247422-T-C
• rs7973431
• ENST00000754393.1:n.445+6578A>G

Variant summary

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

The ENST00000754393.1(ENSG00000257252):​n.445+6578A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,192 control chromosomes in the GnomAD database, including 36,438 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 0.69 (36438 hom., cov: 28)
• Consequence: ENSG00000257252 ENST00000754393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.80
• Publications: 4 publications found

Genes affected

ENSG00000257252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754393.1. 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
	LOC643339	NR_040096.1		n.330-31743A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257252	ENST00000754393.1		n.445+6578A>G		intron	N/A
	ENSG00000257252	ENST00000754394.1		n.394+6578A>G		intron	N/A
	ENSG00000257252	ENST00000754396.1		n.354+6578A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104709 AN: 151082 Hom.: 36410 Cov.: 28

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.693 AC: 104781 AN: 151192 Hom.: 36438 Cov.: 28 AF XY: 0.692 AC XY: 51039 AN XY: 73764

African (AFR) AF: 0.713 AC: 29342 AN: 41174

American (AMR) AF: 0.655 AC: 9959 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2369 AN: 3464

East Asian (EAS) AF: 0.672 AC: 3451 AN: 5132

South Asian (SAS) AF: 0.615 AC: 2925 AN: 4756

European-Finnish (FIN) AF: 0.722 AC: 7438 AN: 10298

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 46953 AN: 67872

Other (OTH) AF: 0.702 AC: 1472 AN: 2096

Alfa AF: 0.692 Hom.: 145718

Bravo AF: 0.688

Asia WGS AF: 0.671 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.011
DANN	Benign	0.39
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs7973431; hg19: chr12-93641198;