rs724078

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;