rs2069522

Variant names:

• chr15-74746892-T-C
• rs2069522

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 0.0542 in 152,260 control chromosomes in the GnomAD database, including 340 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 0.054 (340 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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: 0.0542 AC: 8243 AN: 152142 Hom.: 340 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.0798

Gnomad SAS AF: 0.0861

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0542 AC: 8245 AN: 152260 Hom.: 340 Cov.: 32 AF XY: 0.0555 AC XY: 4133 AN XY: 74444

African (AFR) AF: 0.109 AC: 4511 AN: 41534

American (AMR) AF: 0.0353 AC: 540 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3472

East Asian (EAS) AF: 0.0790 AC: 410 AN: 5188

South Asian (SAS) AF: 0.0868 AC: 418 AN: 4816

European-Finnish (FIN) AF: 0.0487 AC: 517 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1513 AN: 68022

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0333 Hom.: 463

Bravo AF: 0.0541

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.48
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2069522; hg19: chr15-75039233;