rs601339

chr12-122690196-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000543611.1(ENSG00000256249):n.257+2815A>G variant causes a intron, non coding transcript 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: ENST00000543611.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000543611.1	n.257+2815A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.205

Alfa AF: 0.199 Hom.: 2758

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601339; hg19: chr12-123174743;