rs1020661

Variant names:

• chr5-57883677-T-C
• rs1020661

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 0.629 in 152,060 control chromosomes in the GnomAD database, including 30,393 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 0.63 (30393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.693 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: 0.630 AC: 95667 AN: 151942 Hom.: 30396 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.629 AC: 95684 AN: 152060 Hom.: 30393 Cov.: 32 AF XY: 0.630 AC XY: 46810 AN XY: 74312

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.623

Alfa AF: 0.650 Hom.: 61735

Bravo AF: 0.613

Asia WGS AF: 0.630 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1020661; hg19: chr5-57179504;