rs754387

Positions:

• chr6-88169140-A-C
• chr6-88169140-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 0.635 in 152,006 control chromosomes in the GnomAD database, including 30,936 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 0.63 (30936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

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 (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.635 AC: 96440 AN: 151888 Hom.: 30919 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.635 AC: 96507 AN: 152006 Hom.: 30936 Cov.: 32 AF XY: 0.636 AC XY: 47252 AN XY: 74270

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.655

Alfa AF: 0.651 Hom.: 12004

Bravo AF: 0.628

Asia WGS AF: 0.660 AC: 2293 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	0.36
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754387; hg19: chr6-88878859;