rs754387

Variant names:

• chr6-88169140-A-C
• rs754387

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;