6-153913732-G-C

Position:

• chr6-153913732-G-C

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 0.805 in 151,496 control chromosomes in the GnomAD database, including 49,466 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 0.80 (49466 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 121829 AN: 151378 Hom.: 49422 Cov.: 28

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.805 AC: 121928 AN: 151496 Hom.: 49466 Cov.: 28 AF XY: 0.806 AC XY: 59679 AN XY: 74002

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.820

Alfa AF: 0.645 Hom.: 1733

Bravo AF: 0.820

Asia WGS AF: 0.811 AC: 2810 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.10
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6900489; hg19: chr6-154234867;