rs6888329

Variant names:

• chr5-148836839-G-A
• rs6888329

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 0.666 in 152,058 control chromosomes in the GnomAD database, including 34,069 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 0.67 (34069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.666 AC: 101154 AN: 151938 Hom.: 34028 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.666 AC: 101241 AN: 152058 Hom.: 34069 Cov.: 32 AF XY: 0.662 AC XY: 49240 AN XY: 74332

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.678

Alfa AF: 0.659 Hom.: 45655

Bravo AF: 0.664

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6888329; hg19: chr5-148216402;