chr4-186064047-A-G

Variant names:

• chr4-186064047-A-G
• rs6822014

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 0.193 in 152,058 control chromosomes in the GnomAD database, including 2,926 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 0.19 (2926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.193 AC: 29365 AN: 151940 Hom.: 2915 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.193 AC: 29418 AN: 152058 Hom.: 2926 Cov.: 32 AF XY: 0.194 AC XY: 14415 AN XY: 74366

African (AFR) AF: 0.201 AC: 8323 AN: 41480

American (AMR) AF: 0.183 AC: 2793 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3462

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5160

South Asian (SAS) AF: 0.170 AC: 821 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1936 AN: 10590

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13154 AN: 67958

Other (OTH) AF: 0.190 AC: 401 AN: 2110

Alfa AF: 0.189 Hom.: 564

Bravo AF: 0.193

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.47
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6822014; hg19: chr4-186985201;