rs6858430

Positions:

• chr4-174894978-T-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 0.741 in 152,124 control chromosomes in the GnomAD database, including 42,291 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 0.74 (42291 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.174894978T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAM29	ENST00000507969.5	n.345-36008T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112675 AN: 152006 Hom.: 42246 Cov.: 34

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.741 AC: 112777 AN: 152124 Hom.: 42291 Cov.: 34 AF XY: 0.736 AC XY: 54695 AN XY: 74354

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.725

Alfa AF: 0.782 Hom.: 68342

Bravo AF: 0.731

Asia WGS AF: 0.632 AC: 2191 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6858430; hg19: chr4-175816129;