rs6853847

Variant names:

• chr4-91996064-A-C
• rs6853847

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 0.073 in 152,254 control chromosomes in the GnomAD database, including 676 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 0.073 (676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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: 0.0728 AC: 11069 AN: 152136 Hom.: 668 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.00519

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0741

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

GnomAD4 genome AF: 0.0730 AC: 11116 AN: 152254 Hom.: 676 Cov.: 33 AF XY: 0.0708 AC XY: 5269 AN XY: 74454

African (AFR) AF: 0.161 AC: 6700 AN: 41508

American (AMR) AF: 0.0596 AC: 912 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3470

East Asian (EAS) AF: 0.00520 AC: 27 AN: 5190

South Asian (SAS) AF: 0.0918 AC: 443 AN: 4826

European-Finnish (FIN) AF: 0.0221 AC: 235 AN: 10618

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0359 AC: 2441 AN: 68016

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

Alfa AF: 0.0596 Hom.: 52

Bravo AF: 0.0777

Asia WGS AF: 0.0680 AC: 241 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6853847; hg19: chr4-92917215;