rs2752903

Variant names:

• chr20-33235584-T-C
• rs2752903

Your query was ambiguous. Multiple possible variants found:

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

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 0.343 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

GnomAD2 exomes AF: 0.333 AC: 8 AN: 24 AF XY: 0.250

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

African (AFR) AF: 0.629 AC: 26043 AN: 41392

American (AMR) AF: 0.177 AC: 2696 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5150

South Asian (SAS) AF: 0.206 AC: 992 AN: 4812

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10580

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16995 AN: 67956

Other (OTH) AF: 0.295 AC: 624 AN: 2114

Alfa AF: 0.270 Hom.: 24397

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
PhyloP100		-0.94
PromoterAI		0.021	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2752903; hg19: chr20-31823390;