rs7313833

Variant names:

• chr12-27930263-G-A
• rs7313833
• ENST00000825469.1:n.321-28256G>A

Variant summary

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

The ENST00000825469.1(ENSG00000257042):​n.321-28256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,138 control chromosomes in the GnomAD database, including 10,775 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 0.37 (10775 hom., cov: 33)
• Consequence: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 7 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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
ENSG00000257042	ENST00000825469.1	n.321-28256G>A		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1	n.176-28256G>A		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1	n.141-28256G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56338 AN: 152020 Hom.: 10760 Cov.: 33

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.371 AC: 56405 AN: 152138 Hom.: 10775 Cov.: 33 AF XY: 0.371 AC XY: 27629 AN XY: 74392

African (AFR) AF: 0.454 AC: 18842 AN: 41498

American (AMR) AF: 0.335 AC: 5122 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2272 AN: 5186

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4818

European-Finnish (FIN) AF: 0.345 AC: 3656 AN: 10588

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22273 AN: 67984

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.343 Hom.: 1252

Bravo AF: 0.374

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.57
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs7313833; hg19: chr12-28083196;