rs12582659

chr12-75670748-T-C

Variant summary

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

The ENST00000552856.1(ENSG00000258077):n.401+21357A>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 0.0543 in 152,336 control chromosomes in the GnomAD database, including 512 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 0.054 (512 hom., cov: 33)
• Consequence: ENST00000552856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369844	XR_007063375.1	n.1372-6942A>G		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063374.1	n.691+21357A>G		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063376.1	n.2299-6942A>G		intron_variant, non_coding_transcript_variant
LOC105369844	XR_007063377.1	n.2299-6942A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000552856.1	n.401+21357A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000651075.1	n.262-88T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8256 AN: 152218 Hom.: 507 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00883

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0543 AC: 8276 AN: 152336 Hom.: 512 Cov.: 33 AF XY: 0.0590 AC XY: 4392 AN XY: 74500

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.0678

Gnomad4 NFE AF: 0.00883

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0238 Hom.: 25

Bravo AF: 0.0518

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.9
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12582659; hg19: chr12-76064528;