20-31438570-T-A

Variant names:

• chr20-31438570-T-A
• rs17328705

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 0.0784 in 151,114 control chromosomes in the GnomAD database, including 583 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 0.078 (583 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0785 AC: 11853 AN: 150996 Hom.: 584 Cov.: 28

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.0597

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.000980

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0784 AC: 11851 AN: 151114 Hom.: 583 Cov.: 28 AF XY: 0.0755 AC XY: 5574 AN XY: 73854

African (AFR) AF: 0.0442 AC: 1821 AN: 41180

American (AMR) AF: 0.0581 AC: 880 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3456

East Asian (EAS) AF: 0.000982 AC: 5 AN: 5090

South Asian (SAS) AF: 0.0626 AC: 298 AN: 4762

European-Finnish (FIN) AF: 0.0712 AC: 740 AN: 10394

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7251 AN: 67794

Other (OTH) AF: 0.0871 AC: 182 AN: 2090

Alfa AF: 0.0976 Hom.: 94

Bravo AF: 0.0765

Asia WGS AF: 0.0260 AC: 92 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	3.9
DANN	Benign	0.82
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs17328705; hg19: chr20-30026373;