rs870431

Variant names:

• chr12-38559271-T-C
• rs870431
• ENST00000552639.1:n.200-12763A>G

Variant summary

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

The ENST00000552639.1(ENSG00000258119):​n.200-12763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,060 control chromosomes in the GnomAD database, including 10,542 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 0.35 (10542 hom., cov: 32)
• Consequence: ENSG00000258119 ENST00000552639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

Genes affected

ENSG00000258119 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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
ENSG00000258119	ENST00000552639.1	n.200-12763A>G		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52751 AN: 151942 Hom.: 10549 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.347 AC: 52737 AN: 152060 Hom.: 10542 Cov.: 32 AF XY: 0.344 AC XY: 25608 AN XY: 74342

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.394

Alfa AF: 0.428 Hom.: 7973

Bravo AF: 0.330

Asia WGS AF: 0.284 AC: 987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870431; hg19: chr12-38953073;