rs1780616

Variant names:

• chr20-38344539-T-C
• rs1780616

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.611 AC: 25312 AN: 41448

American (AMR) AF: 0.584 AC: 8929 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2169 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2815 AN: 5168

South Asian (SAS) AF: 0.674 AC: 3246 AN: 4818

European-Finnish (FIN) AF: 0.633 AC: 6691 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44547 AN: 67974

Other (OTH) AF: 0.608 AC: 1282 AN: 2108

Alfa AF: 0.647 Hom.: 3953

Bravo AF: 0.619

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1780616; hg19: chr20-36972942;