rs6857229

Variant names:

• chr4-75566358-G-A
• rs6857229

Your query was ambiguous. Multiple possible variants found:

• chr4-75566358-G-A
• chr4-75566358-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 0.253 in 152,110 control chromosomes in the GnomAD database, including 5,100 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 0.25 (5100 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.253 AC: 38499 AN: 151992 Hom.: 5093 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.253 AC: 38523 AN: 152110 Hom.: 5100 Cov.: 33 AF XY: 0.257 AC XY: 19139 AN XY: 74348

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.257

Alfa AF: 0.227 Hom.: 8504

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6857229; hg19: chr4-76491568;