rs6857038

Positions:

• chr4-34356334-G-A

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 0.278 in 152,022 control chromosomes in the GnomAD database, including 7,589 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 0.28 (7589 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34356334G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42199 AN: 151904 Hom.: 7575 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.278 AC: 42254 AN: 152022 Hom.: 7589 Cov.: 32 AF XY: 0.280 AC XY: 20817 AN XY: 74304

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.246

Alfa AF: 0.239 Hom.: 654

Bravo AF: 0.288

Asia WGS AF: 0.292 AC: 1012 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.047
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6857038; hg19: chr4-34357956;