rs13209234

Variant names:

• chr6-32448198-G-A
• rs13209234

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 0.127 in 151,932 control chromosomes in the GnomAD database, including 1,415 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 0.13 (1415 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.127 AC: 19296 AN: 151818 Hom.: 1415 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0618

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.127 AC: 19314 AN: 151932 Hom.: 1415 Cov.: 32 AF XY: 0.131 AC XY: 9690 AN XY: 74236

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0618

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.123

Alfa AF: 0.134 Hom.: 1060

Bravo AF: 0.117

Asia WGS AF: 0.0970 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.39
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13209234; hg19: chr6-32415975;