chr13-77399366-A-G

Variant names:

• chr13-77399366-A-G
• rs9530646
• ENST00000783822.1:n.75+12257A>G

Variant summary

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

The ENST00000783822.1(ENSG00000285714):​n.75+12257A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,174 control chromosomes in the GnomAD database, including 20,763 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 0.47 (20763 hom., cov: 33)
• Consequence: ENSG00000285714 ENST00000783822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 2 publications found

Genes affected

ENSG00000285714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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
ENSG00000285714	ENST00000783822.1	n.75+12257A>G		intron_variant	Intron 1 of 2
ENSG00000285714	ENST00000783823.1	n.251+9891A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70838 AN: 152056 Hom.: 20773 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.465 AC: 70824 AN: 152174 Hom.: 20763 Cov.: 33 AF XY: 0.460 AC XY: 34263 AN XY: 74410

African (AFR) AF: 0.113 AC: 4705 AN: 41548

American (AMR) AF: 0.449 AC: 6871 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1374 AN: 5162

South Asian (SAS) AF: 0.435 AC: 2098 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6489 AN: 10586

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45316 AN: 67980

Other (OTH) AF: 0.492 AC: 1041 AN: 2114

Alfa AF: 0.555 Hom.: 3792

Bravo AF: 0.437

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.37
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs9530646; hg19: chr13-77973501;