rs331615

Variant names:

• chr20-57063481-T-A
• rs331615

Your query was ambiguous. Multiple possible variants found:

• chr20-57063481-T-A
• chr20-57063481-T-C
• chr20-57063481-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 0.445 in 151,848 control chromosomes in the GnomAD database, including 15,294 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 0.45 (15294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 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: 0.445 AC: 67518 AN: 151730 Hom.: 15267 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.445 AC: 67579 AN: 151848 Hom.: 15294 Cov.: 31 AF XY: 0.440 AC XY: 32704 AN XY: 74244

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.487

Alfa AF: 0.434 Hom.: 7898

Bravo AF: 0.468

Asia WGS AF: 0.468 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs331615; hg19: chr20-55638537;