rs6843849

Variant names:

• chr4-157448278-G-A
• rs6843849

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 0.554 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.553 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

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.533

Alfa AF: 0.514 Hom.: 2631

Bravo AF: 0.560

Asia WGS AF: 0.421 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6843849; hg19: chr4-158369430;