chr4-160183148-G-A

Variant names:

• chr4-160183148-G-A
• rs6827285

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 0.265 in 151,702 control chromosomes in the GnomAD database, including 5,934 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 0.26 (5934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40142 AN: 151584 Hom.: 5920 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.265 AC: 40196 AN: 151702 Hom.: 5934 Cov.: 32 AF XY: 0.258 AC XY: 19117 AN XY: 74136

African (AFR) AF: 0.402 AC: 16617 AN: 41384

American (AMR) AF: 0.198 AC: 3006 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3468

East Asian (EAS) AF: 0.0862 AC: 445 AN: 5164

South Asian (SAS) AF: 0.128 AC: 617 AN: 4820

European-Finnish (FIN) AF: 0.200 AC: 2111 AN: 10536

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15856 AN: 67804

Other (OTH) AF: 0.231 AC: 487 AN: 2106

Alfa AF: 0.242 Hom.: 1142

Bravo AF: 0.272

Asia WGS AF: 0.128 AC: 444 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.78
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6827285; hg19: chr4-161104300; COSMIC: COSV67093145;