rs7569328

Variant names:

• chr2-20901018-C-T
• rs7569328

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 0.0546 in 152,152 control chromosomes in the GnomAD database, including 525 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 0.055 (525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 12 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 (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.0546 AC: 8296 AN: 152034 Hom.: 524 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0546 AC: 8314 AN: 152152 Hom.: 525 Cov.: 32 AF XY: 0.0534 AC XY: 3974 AN XY: 74382

African (AFR) AF: 0.152 AC: 6306 AN: 41500

American (AMR) AF: 0.0258 AC: 395 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3466

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5152

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4822

European-Finnish (FIN) AF: 0.0136 AC: 144 AN: 10604

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 981 AN: 68008

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0314 Hom.: 503

Bravo AF: 0.0592

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7569328; hg19: chr2-21100778;