rs6846167

Positions:

• chr4-167915543-A-T

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 0.279 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0956

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.293

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6846167; hg19: chr4-168836694;