rs9506995

Positions:

• chr13-23001016-G-C
• chr13-23001016-G-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23001016G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.239

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9506995; hg19: chr13-23575155;