chr13-86166464-C-A

Position:

• chr13-86166464-C-A

Variant summary

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

The ENST00000445967.1(ENSG00000232252):​n.149-4381C>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 0.53 in 151,992 control chromosomes in the GnomAD database, including 21,480 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 0.53 (21480 hom., cov: 32)
• Consequence: ENST00000445967.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000445967.1	n.149-4381C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80485 AN: 151874 Hom.: 21455 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.530 AC: 80572 AN: 151992 Hom.: 21480 Cov.: 32 AF XY: 0.530 AC XY: 39341 AN XY: 74276

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.514

Alfa AF: 0.516 Hom.: 39362

Bravo AF: 0.523

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7326634; hg19: chr13-86740599;