chr6-52185988-A-G

Variant names:

• chr6-52185988-A-G
• rs3819024

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 0.343 in 152,016 control chromosomes in the GnomAD database, including 9,284 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 0.34 (9284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 74 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52183 AN: 151898 Hom.: 9283 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.343 AC: 52192 AN: 152016 Hom.: 9284 Cov.: 32 AF XY: 0.346 AC XY: 25707 AN XY: 74294

African (AFR) AF: 0.287 AC: 11903 AN: 41446

American (AMR) AF: 0.259 AC: 3953 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2507 AN: 5158

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4645 AN: 10546

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25062 AN: 67996

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.343 Hom.: 14902

Bravo AF: 0.324

Asia WGS AF: 0.392 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		0.24
PromoterAI		-0.0031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3819024; hg19: chr6-52050786;