rs2752903

Positions:

• chr20-33235584-T-C
• chr20-33235584-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.343 in 151,948 control chromosomes in the GnomAD database, including 11,472 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 0.34 (11472 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51950 AN: 151828 Hom.: 11428 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.292

GnomAD3 exomes AF: 0.333 AC: 8 AN: 24 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad AFR exome AF: 0.500

Gnomad NFE exome AF: 0.278

Gnomad OTH exome AF: 0.500

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

GnomAD4 genome AF: 0.343 AC: 52061 AN: 151948 Hom.: 11472 Cov.: 31 AF XY: 0.338 AC XY: 25093 AN XY: 74262

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.295

Alfa AF: 0.242 Hom.: 7952

Bravo AF: 0.349

Asia WGS AF: 0.263 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2752903; hg19: chr20-31823390;