rs1780616

Variant names:

• chr20-38344539-T-C
• rs1780616

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 0.63 in 152,044 control chromosomes in the GnomAD database, including 30,326 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 (30326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 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: 95759 AN: 151926 Hom.: 30313 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.630 AC: 95810 AN: 152044 Hom.: 30326 Cov.: 32 AF XY: 0.628 AC XY: 46674 AN XY: 74336

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.608

Alfa AF: 0.647 Hom.: 3953

Bravo AF: 0.619

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1780616; hg19: chr20-36972942;