rs6889746

Variant names:

• chr5-52411072-A-G
• rs6889746

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 0.291 in 151,994 control chromosomes in the GnomAD database, including 7,720 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 0.29 (7720 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.292 AC: 44296 AN: 151876 Hom.: 7723 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.291 AC: 44294 AN: 151994 Hom.: 7720 Cov.: 31 AF XY: 0.293 AC XY: 21794 AN XY: 74272

African (AFR) AF: 0.102 AC: 4212 AN: 41486

American (AMR) AF: 0.319 AC: 4862 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1443 AN: 5152

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4824

European-Finnish (FIN) AF: 0.434 AC: 4578 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25837 AN: 67940

Other (OTH) AF: 0.295 AC: 624 AN: 2114

Alfa AF: 0.336 Hom.: 19717

Bravo AF: 0.274

Asia WGS AF: 0.245 AC: 853 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	0.97
DANN	Benign	0.50
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs6889746; hg19: chr5-51706906; COSMIC: COSV50460062;