chr4-34356334-G-A

Variant names:

• chr4-34356334-G-A
• rs6857038

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.510 AC: 21152 AN: 41482

American (AMR) AF: 0.254 AC: 3871 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1005 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1526 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10548

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11437 AN: 67948

Other (OTH) AF: 0.246 AC: 519 AN: 2110

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs6857038; hg19: chr4-34357956;