rs13204672

chr6-32615019-A-G

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 0.124 in 152,214 control chromosomes in the GnomAD database, including 1,324 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 0.12 (1324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18883 AN: 152096 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.124 AC: 18875 AN: 152214 Hom.: 1324 Cov.: 32 AF XY: 0.119 AC XY: 8888 AN XY: 74428

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0424

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0551

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.146

Alfa AF: 0.132 Hom.: 754

Bravo AF: 0.131

Asia WGS AF: 0.0800 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13204672; hg19: chr6-32582796;