chr13-46999481-A-G

Variant names:

• chr13-46999481-A-G
• rs12583882
• ENST00000778995.1:n.112-22166A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000778995.1(ENSG00000301465):​n.112-22166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,120 control chromosomes in the GnomAD database, including 6,602 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 0.27 (6602 hom., cov: 32)
• Consequence: ENSG00000301465 ENST00000778995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 4 publications found

Genes affected

ENSG00000301465 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778995.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301465	ENST00000778995.1		n.112-22166A>G		intron	N/A
	ENSG00000301465	ENST00000778996.1		n.123-22166A>G		intron	N/A
	ENSG00000301465	ENST00000778997.1		n.121-22166A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40771 AN: 152002 Hom.: 6591 Cov.: 32

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.268 AC: 40792 AN: 152120 Hom.: 6602 Cov.: 32 AF XY: 0.274 AC XY: 20384 AN XY: 74332

African (AFR) AF: 0.0820 AC: 3405 AN: 41538

American (AMR) AF: 0.314 AC: 4797 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2233 AN: 5162

South Asian (SAS) AF: 0.290 AC: 1397 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4226 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22644 AN: 67968

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.304 Hom.: 15543

Bravo AF: 0.252

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs12583882; hg19: chr13-47573616;