rs6848139

Variant names:

• chr4-122473886-A-C
• rs6848139

Your query was ambiguous. Multiple possible variants found:

• chr4-122473886-A-C
• chr4-122473886-A-G

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 0.164 in 151,994 control chromosomes in the GnomAD database, including 3,590 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 0.16 (3590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24814 AN: 151876 Hom.: 3577 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.164 AC: 24852 AN: 151994 Hom.: 3590 Cov.: 32 AF XY: 0.162 AC XY: 12003 AN XY: 74320

African (AFR) AF: 0.389 AC: 16107 AN: 41362

American (AMR) AF: 0.0836 AC: 1277 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0544 AC: 189 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.0617 AC: 298 AN: 4830

European-Finnish (FIN) AF: 0.0954 AC: 1010 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0823 AC: 5598 AN: 67982

Other (OTH) AF: 0.140 AC: 295 AN: 2114

Alfa AF: 0.107 Hom.: 3049

Bravo AF: 0.170

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.45
DANN	Benign	0.70
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6848139; hg19: chr4-123395041;