13-86126868-A-G

Position:

• chr13-86126868-A-G

Variant summary

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

The ENST00000445967.1(ENSG00000232252):​n.149-43977A>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 0.59 in 151,998 control chromosomes in the GnomAD database, including 27,038 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 0.59 (27038 hom., cov: 32)
• Consequence: ENST00000445967.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 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
	ENST00000445967.1	n.149-43977A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89607 AN: 151882 Hom.: 27002 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.590 AC: 89691 AN: 151998 Hom.: 27038 Cov.: 32 AF XY: 0.590 AC XY: 43787 AN XY: 74278

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.550

Alfa AF: 0.551 Hom.: 10565

Bravo AF: 0.587

Asia WGS AF: 0.453 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413455; hg19: chr13-86701003;