rs1780616

Positions:

• chr20-38344539-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 0.63 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;