rs6843849

Variant names:

• chr4-157448278-G-A
• rs6843849

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 0.554 in 151,930 control chromosomes in the GnomAD database, including 25,129 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 0.55 (25129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.553 AC: 83998 AN: 151812 Hom.: 25084 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.554 AC: 84099 AN: 151930 Hom.: 25129 Cov.: 32 AF XY: 0.550 AC XY: 40809 AN XY: 74246

African (AFR) AF: 0.803 AC: 33290 AN: 41468

American (AMR) AF: 0.432 AC: 6594 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5144

South Asian (SAS) AF: 0.404 AC: 1944 AN: 4812

European-Finnish (FIN) AF: 0.498 AC: 5249 AN: 10548

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31955 AN: 67928

Other (OTH) AF: 0.533 AC: 1124 AN: 2108

Alfa AF: 0.525 Hom.: 2878

Bravo AF: 0.560

Asia WGS AF: 0.421 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6843849; hg19: chr4-158369430;