chr4-167915543-A-T

Variant names:

• chr4-167915543-A-T
• rs6846167

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 0.279 in 152,068 control chromosomes in the GnomAD database, including 6,558 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 (6558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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: 0.279 AC: 42333 AN: 151950 Hom.: 6552 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.279 AC: 42362 AN: 152068 Hom.: 6558 Cov.: 32 AF XY: 0.269 AC XY: 20016 AN XY: 74338

African (AFR) AF: 0.387 AC: 16041 AN: 41492

American (AMR) AF: 0.211 AC: 3225 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.0956 AC: 495 AN: 5176

South Asian (SAS) AF: 0.139 AC: 669 AN: 4826

European-Finnish (FIN) AF: 0.161 AC: 1705 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18191 AN: 67914

Other (OTH) AF: 0.293 AC: 618 AN: 2112

Alfa AF: 0.269 Hom.: 748

Bravo AF: 0.289

Asia WGS AF: 0.120 AC: 417 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.62
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6846167; hg19: chr4-168836694;