rs1321309

chr6-36670859-G-Achr6-36670859-G-Cchr6-36670859-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 0.382 in 152,070 control chromosomes in the GnomAD database, including 12,572 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 0.38 (12572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 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: 0.382 AC: 58069 AN: 151950 Hom.: 12577 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.382 AC: 58054 AN: 152070 Hom.: 12572 Cov.: 32 AF XY: 0.382 AC XY: 28393 AN XY: 74328

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.348

Alfa AF: 0.446 Hom.: 9105

Bravo AF: 0.354

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	13
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321309; hg19: chr6-36638636;