chr13-47672039-A-G

Variant names:

• chr13-47672039-A-G
• rs10507559
• ENST00000765501.1:n.80-37076A>G

Variant summary

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

The ENST00000765501.1(ENSG00000299661):​n.80-37076A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,108 control chromosomes in the GnomAD database, including 8,932 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 0.31 (8932 hom., cov: 32)
• Consequence: ENSG00000299661 ENST00000765501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

Genes affected

ENSG00000299661 (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 (EAS) allele frequency at 95% confidence interval = 0.461 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
ENSG00000299661	ENST00000765501.1	n.80-37076A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47169 AN: 151990 Hom.: 8931 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.310 AC: 47178 AN: 152108 Hom.: 8932 Cov.: 32 AF XY: 0.314 AC XY: 23368 AN XY: 74342

African (AFR) AF: 0.0928 AC: 3855 AN: 41536

American (AMR) AF: 0.382 AC: 5842 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 969 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2458 AN: 5154

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4820

European-Finnish (FIN) AF: 0.443 AC: 4681 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26658 AN: 67962

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.367 Hom.: 5557

Bravo AF: 0.301

Asia WGS AF: 0.380 AC: 1320 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.43
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10507559; hg19: chr13-48246174;