rs852004

Variant names:

• chr6-151639281-C-T
• rs852004

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 0.198 in 152,128 control chromosomes in the GnomAD database, including 3,647 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 0.20 (3647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.198 AC: 30108 AN: 152010 Hom.: 3644 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.198 AC: 30128 AN: 152128 Hom.: 3647 Cov.: 32 AF XY: 0.199 AC XY: 14814 AN XY: 74328

African (AFR) AF: 0.0715 AC: 2969 AN: 41538

American (AMR) AF: 0.190 AC: 2896 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3468

East Asian (EAS) AF: 0.0724 AC: 375 AN: 5180

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4812

European-Finnish (FIN) AF: 0.318 AC: 3355 AN: 10544

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17686 AN: 67998

Other (OTH) AF: 0.193 AC: 407 AN: 2108

Alfa AF: 0.229 Hom.: 588

Bravo AF: 0.181

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs852004; hg19: chr6-151960416;