rs4713274

Positions:

• chr6-29969716-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 0.235 in 151,924 control chromosomes in the GnomAD database, including 4,742 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 0.23 (4742 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29969716G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35674 AN: 151808 Hom.: 4742 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.235 AC: 35670 AN: 151924 Hom.: 4742 Cov.: 32 AF XY: 0.235 AC XY: 17461 AN XY: 74246

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.207

Alfa AF: 0.267 Hom.: 770

Bravo AF: 0.223

Asia WGS AF: 0.189 AC: 652 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713274; hg19: chr6-29937493;