chr13-23001016-G-C

Variant names:

• chr13-23001016-G-C
• rs9506995

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 0.26 in 152,026 control chromosomes in the GnomAD database, including 5,837 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 0.26 (5837 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39457 AN: 151908 Hom.: 5834 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.260 AC: 39464 AN: 152026 Hom.: 5837 Cov.: 31 AF XY: 0.263 AC XY: 19522 AN XY: 74292

African (AFR) AF: 0.133 AC: 5506 AN: 41480

American (AMR) AF: 0.392 AC: 5988 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1483 AN: 5154

South Asian (SAS) AF: 0.249 AC: 1195 AN: 4804

European-Finnish (FIN) AF: 0.278 AC: 2938 AN: 10564

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20633 AN: 67970

Other (OTH) AF: 0.239 AC: 504 AN: 2112

Alfa AF: 0.155 Hom.: 325

Bravo AF: 0.264

Asia WGS AF: 0.281 AC: 976 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	7.9
DANN	Benign	0.81
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9506995; hg19: chr13-23575155;