rs9570136

Variant names:

• chr13-59464929-A-G
• rs9570136
• ENST00000719077.1:n.437+4996A>G

Variant summary

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

The ENST00000719077.1(ENSG00000293794):​n.437+4996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,106 control chromosomes in the GnomAD database, including 8,172 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 0.32 (8172 hom., cov: 32)
• Consequence: ENSG00000293794 ENST00000719077.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 0 publications found

Genes affected

ENSG00000293794 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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
ENSG00000293794	ENST00000719077.1	n.437+4996A>G		intron_variant	Intron 2 of 2
ENSG00000293794	ENST00000719078.1	n.224+4996A>G		intron_variant	Intron 2 of 2
ENSG00000293794	ENST00000719079.1	n.301+4996A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49139 AN: 151988 Hom.: 8171 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.323 AC: 49172 AN: 152106 Hom.: 8172 Cov.: 32 AF XY: 0.319 AC XY: 23718 AN XY: 74352

African (AFR) AF: 0.304 AC: 12619 AN: 41492

American (AMR) AF: 0.317 AC: 4848 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3472

East Asian (EAS) AF: 0.0917 AC: 475 AN: 5178

South Asian (SAS) AF: 0.237 AC: 1147 AN: 4830

European-Finnish (FIN) AF: 0.324 AC: 3425 AN: 10570

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24404 AN: 67960

Other (OTH) AF: 0.339 AC: 714 AN: 2108

Alfa AF: 0.350 Hom.: 4975

Bravo AF: 0.322

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs9570136; hg19: chr13-60039063;