rs6989593

Variant names:

• chr8-46639634-A-G
• rs6989593

Your query was ambiguous. Multiple possible variants found:

• chr8-46639634-A-G
• chr8-46639634-A-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 0.513 in 151,834 control chromosomes in the GnomAD database, including 24,385 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 0.51 (24385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

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 (NFE) allele frequency at 95% confidence interval = 0.693 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: 0.514 AC: 77908 AN: 151716 Hom.: 24389 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.513 AC: 77897 AN: 151834 Hom.: 24385 Cov.: 32 AF XY: 0.510 AC XY: 37826 AN XY: 74180

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.536

Alfa AF: 0.661 Hom.: 42596

Bravo AF: 0.492

Asia WGS AF: 0.477 AC: 1660 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	6.2
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6989593; hg19: chr8-47551256;