rs724078

Variant names:

• chr6-29521271-G-A
• rs724078

Your query was ambiguous. Multiple possible variants found:

• chr6-29521271-G-A
• chr6-29521271-G-C

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 0.412 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.411 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

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.425

Alfa AF: 0.327 Hom.: 10793

Bravo AF: 0.412

Asia WGS AF: 0.475 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724078; hg19: chr6-29489048;