rs13212921

chr6-27237643-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0846 in 152,276 control chromosomes in the GnomAD database, including 645 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 0.085 (645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0846 AC: 12880 AN: 152158 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0194

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0846 AC: 12885 AN: 152276 Hom.: 645 Cov.: 32 AF XY: 0.0799 AC XY: 5951 AN XY: 74458

Gnomad4 AFR AF: 0.0740

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0190

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.100 Hom.: 738

Bravo AF: 0.0825

Asia WGS AF: 0.0170 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	7.4
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13212921; hg19: chr6-27205422;