chr12-89932155-G-A

Position:

• chr12-89932155-G-A

Variant summary

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

The ENST00000651272.1(ENSG00000258216):​n.504+10986G>A 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 0.252 in 151,894 control chromosomes in the GnomAD database, including 5,580 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 0.25 (5580 hom., cov: 32)
• Consequence: ENST00000651272.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369890	XR_001749246.2	n.456-881G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651272.1	n.504+10986G>A		intron_variant, non_coding_transcript_variant
	ENST00000547370.5	n.331-3667G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000549551.1	n.172+10986G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38354 AN: 151776 Hom.: 5583 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.252 AC: 38343 AN: 151894 Hom.: 5580 Cov.: 32 AF XY: 0.256 AC XY: 18990 AN XY: 74240

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.274

Alfa AF: 0.278 Hom.: 3014

Bravo AF: 0.254

Asia WGS AF: 0.466 AC: 1618 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777211; hg19: chr12-90325932;