13-59245009-T-C

Variant names:

• chr13-59245009-T-C
• rs9570077
• ENST00000829268.1:n.360-28834A>G

Variant summary

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

The ENST00000829268.1(ENSG00000307835):​n.360-28834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,094 control chromosomes in the GnomAD database, including 5,027 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 0.24 (5027 hom., cov: 32)
• Consequence: ENSG00000307835 ENST00000829268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 1 publications found

Genes affected

ENSG00000307835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829268.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307835	ENST00000829268.1		n.360-28834A>G		intron	N/A
	ENSG00000307835	ENST00000829269.1		n.558+27222A>G		intron	N/A
	ENSG00000307835	ENST00000829270.1		n.263+27222A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36148 AN: 151976 Hom.: 5028 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.238 AC: 36153 AN: 152094 Hom.: 5027 Cov.: 32 AF XY: 0.236 AC XY: 17537 AN XY: 74360

African (AFR) AF: 0.138 AC: 5724 AN: 41490

American (AMR) AF: 0.191 AC: 2913 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3472

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5178

South Asian (SAS) AF: 0.228 AC: 1102 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3369 AN: 10556

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21529 AN: 67982

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.161 Hom.: 371

Bravo AF: 0.222

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9570077;

hg19: chr13-59819143;