rs870431

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000258119 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.156 AC: 6465 AN: 41524

American (AMR) AF: 0.331 AC: 5056 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1150 AN: 5160

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4820

European-Finnish (FIN) AF: 0.395 AC: 4170 AN: 10566

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31176 AN: 67928

Other (OTH) AF: 0.394 AC: 833 AN: 2112

Alfa AF: 0.390 Hom.: 12593

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs870431; hg19: chr12-38953073;