6-29521271-G-A

Variant names:

• chr6-29521271-G-A
• rs724078

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.412 in 151,924 control chromosomes in the GnomAD database, including 13,712 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 0.41 (13712 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62453 AN: 151804 Hom.: 13670 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.412 AC: 62539 AN: 151924 Hom.: 13712 Cov.: 32 AF XY: 0.416 AC XY: 30868 AN XY: 74254

African (AFR) AF: 0.564 AC: 23355 AN: 41408

American (AMR) AF: 0.387 AC: 5909 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1192 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1445 AN: 5156

South Asian (SAS) AF: 0.464 AC: 2233 AN: 4816

European-Finnish (FIN) AF: 0.440 AC: 4652 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22495 AN: 67912

Other (OTH) AF: 0.425 AC: 899 AN: 2114

Alfa AF: 0.345 Hom.: 32248

Bravo AF: 0.412

Asia WGS AF: 0.475 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.32
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs724078; hg19: chr6-29489048;