rs6844851

chr4-179766847-C-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 0.472 in 151,862 control chromosomes in the GnomAD database, including 18,414 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 0.47 (18414 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71567 AN: 151744 Hom.: 18372 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.472 AC: 71665 AN: 151862 Hom.: 18414 Cov.: 31 AF XY: 0.475 AC XY: 35262 AN XY: 74198

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.482

Alfa AF: 0.385 Hom.: 25779

Bravo AF: 0.493

Asia WGS AF: 0.500 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.083
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: rs6844851; hg19: chr4-180688000;