rs17328705

Variant names:

• chr20-31438570-T-A
• rs17328705

Your query was ambiguous. Multiple possible variants found:

• chr20-31438570-T-A
• chr20-31438570-T-C

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 0.0784 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.000982

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0871

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17328705; hg19: chr20-30026373;