rs9567004

Variant names:

• chr13-42617431-A-G
• rs9567004

Variant summary

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

The variant allele was found at a frequency of 0.0967 in 152,008 control chromosomes in the GnomAD database, including 1,838 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 0.097 (1838 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.289 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

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14640 AN: 151890 Hom.: 1819 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0444

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0797

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

GnomAD4 genome AF: 0.0967 AC: 14700 AN: 152008 Hom.: 1838 Cov.: 31 AF XY: 0.0944 AC XY: 7012 AN XY: 74310

African (AFR) AF: 0.293 AC: 12123 AN: 41384

American (AMR) AF: 0.0509 AC: 778 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5176

South Asian (SAS) AF: 0.0444 AC: 214 AN: 4816

European-Finnish (FIN) AF: 0.00302 AC: 32 AN: 10602

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0167 AC: 1135 AN: 67978

Other (OTH) AF: 0.0788 AC: 166 AN: 2106

Alfa AF: 0.0948 Hom.: 271

Bravo AF: 0.107

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9567004; hg19: chr13-43191567;