chr6-132571801-A-G

Variant names:

• chr6-132571801-A-G
• rs11154685

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 0.309 in 151,374 control chromosomes in the GnomAD database, including 7,372 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 0.31 (7372 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 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: 0.309 AC: 46759 AN: 151256 Hom.: 7366 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.309 AC: 46797 AN: 151374 Hom.: 7372 Cov.: 31 AF XY: 0.314 AC XY: 23183 AN XY: 73936

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.340

Alfa AF: 0.302 Hom.: 5473

Bravo AF: 0.308

Asia WGS AF: 0.398 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11154685; hg19: chr6-132892940; COSMIC: COSV51582585;