1-20557323-C-T

Variant names:

• chr1-20557323-C-T
• rs677214

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 0.796 in 152,060 control chromosomes in the GnomAD database, including 48,515 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 0.80 (48515 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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: 0.796 AC: 120898 AN: 151942 Hom.: 48473 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.796 AC: 120993 AN: 152060 Hom.: 48515 Cov.: 31 AF XY: 0.799 AC XY: 59369 AN XY: 74316

African (AFR) AF: 0.684 AC: 28364 AN: 41458

American (AMR) AF: 0.867 AC: 13246 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3038 AN: 3472

East Asian (EAS) AF: 0.925 AC: 4784 AN: 5172

South Asian (SAS) AF: 0.819 AC: 3932 AN: 4800

European-Finnish (FIN) AF: 0.835 AC: 8830 AN: 10570

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56057 AN: 67994

Other (OTH) AF: 0.817 AC: 1726 AN: 2112

Alfa AF: 0.823 Hom.: 78280

Bravo AF: 0.794

Asia WGS AF: 0.886 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.49
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs677214; hg19: chr1-20883816;