20-38346109-C-G

Variant names:

• chr20-38346109-C-G
• rs2232575

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 0.836 in 152,214 control chromosomes in the GnomAD database, including 53,290 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 0.84 (53290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127117 AN: 152096 Hom.: 53268 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.836 AC: 127193 AN: 152214 Hom.: 53290 Cov.: 32 AF XY: 0.833 AC XY: 62028 AN XY: 74426

African (AFR) AF: 0.865 AC: 35901 AN: 41526

American (AMR) AF: 0.873 AC: 13346 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2829 AN: 3470

East Asian (EAS) AF: 0.752 AC: 3893 AN: 5176

South Asian (SAS) AF: 0.698 AC: 3361 AN: 4818

European-Finnish (FIN) AF: 0.843 AC: 8938 AN: 10598

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56014 AN: 68018

Other (OTH) AF: 0.852 AC: 1799 AN: 2112

Alfa AF: 0.797 Hom.: 2442

Bravo AF: 0.842

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
PhyloP100		-3.3
PromoterAI		-0.17	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2232575; hg19: chr20-36974512;