rs601339

Variant names:

• chr12-122690196-A-G
• rs601339
• ENST00000543611.1:n.257+2815A>G

Variant summary

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

The ENST00000543611.1(ENSG00000256249):​n.257+2815A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,580 control chromosomes in the GnomAD database, including 4,308 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 0.23 (4308 hom., cov: 30)
• Consequence: ENSG00000256249 ENST00000543611.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 27 publications found

Genes affected

ENSG00000256249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 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
ENSG00000256249	ENST00000543611.1	n.257+2815A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34201 AN: 151462 Hom.: 4304 Cov.: 30

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.0889

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.226 AC: 34222 AN: 151580 Hom.: 4308 Cov.: 30 AF XY: 0.222 AC XY: 16465 AN XY: 74072

African (AFR) AF: 0.309 AC: 12765 AN: 41320

American (AMR) AF: 0.193 AC: 2928 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2542 AN: 5108

South Asian (SAS) AF: 0.0894 AC: 430 AN: 4810

European-Finnish (FIN) AF: 0.163 AC: 1716 AN: 10522

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12662 AN: 67852

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.204 Hom.: 10182

Bravo AF: 0.238

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.48
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs601339; hg19: chr12-123174743;