rs2052028

Variant names:

• chr7-15976238-G-C
• rs2052028

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 0.244 in 152,042 control chromosomes in the GnomAD database, including 5,382 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 0.24 (5382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.332 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: 0.244 AC: 37121 AN: 151924 Hom.: 5386 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0122

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.244 AC: 37113 AN: 152042 Hom.: 5382 Cov.: 32 AF XY: 0.241 AC XY: 17876 AN XY: 74306

African (AFR) AF: 0.110 AC: 4549 AN: 41518

American (AMR) AF: 0.219 AC: 3341 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3472

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5170

South Asian (SAS) AF: 0.224 AC: 1077 AN: 4814

European-Finnish (FIN) AF: 0.306 AC: 3234 AN: 10558

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22779 AN: 67940

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.287 Hom.: 849

Bravo AF: 0.233

Asia WGS AF: 0.0990 AC: 344 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	2.5
DANN	Benign	0.56
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2052028; hg19: chr7-16015863;