rs7973458

Variant names:

• chr12-8895294-T-C
• rs7973458
• ENST00000631830.1:n.321+19662A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-8895294-T-C
• chr12-8895294-T-G

Variant summary

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

The ENST00000631830.1(ENSG00000282022):​n.321+19662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,912 control chromosomes in the GnomAD database, including 13,200 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 0.41 (13200 hom., cov: 31)
• Consequence: ENSG00000282022 ENST00000631830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83
• Publications: 9 publications found

Genes affected

ENSG00000282022 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631830.1. 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
	ENSG00000282022	ENST00000631830.1	TSL:3	n.321+19662A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62883 AN: 151792 Hom.: 13182 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.414 AC: 62940 AN: 151912 Hom.: 13200 Cov.: 31 AF XY: 0.415 AC XY: 30822 AN XY: 74234

African (AFR) AF: 0.420 AC: 17423 AN: 41438

American (AMR) AF: 0.451 AC: 6872 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1830 AN: 5162

South Asian (SAS) AF: 0.413 AC: 1993 AN: 4824

European-Finnish (FIN) AF: 0.450 AC: 4737 AN: 10520

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27787 AN: 67944

Other (OTH) AF: 0.382 AC: 806 AN: 2110

Alfa AF: 0.401 Hom.: 46756

Bravo AF: 0.413

Asia WGS AF: 0.415 AC: 1439 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	0.66
DANN	Benign	0.48
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs7973458; hg19: chr12-9047890;