rs573301

Variant names:

• chr6-23922478-C-G
• rs573301

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 0.54 in 151,978 control chromosomes in the GnomAD database, including 23,064 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 0.54 (23064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.540 AC: 81988 AN: 151860 Hom.: 23043 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.540 AC: 82050 AN: 151978 Hom.: 23064 Cov.: 32 AF XY: 0.526 AC XY: 39099 AN XY: 74288

African (AFR) AF: 0.649 AC: 26909 AN: 41480

American (AMR) AF: 0.391 AC: 5959 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1692 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5166

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4814

European-Finnish (FIN) AF: 0.483 AC: 5091 AN: 10548

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38188 AN: 67938

Other (OTH) AF: 0.500 AC: 1056 AN: 2110

Alfa AF: 0.554 Hom.: 2939

Bravo AF: 0.537

Asia WGS AF: 0.288 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.75
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs573301; hg19: chr6-23922706;