20-46172387-A-G

Variant names:

• chr20-46172387-A-G
• rs1321000

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 0.738 in 152,066 control chromosomes in the GnomAD database, including 42,020 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 0.74 (42020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 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: 0.738 AC: 112157 AN: 151948 Hom.: 41963 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.738 AC: 112265 AN: 152066 Hom.: 42020 Cov.: 31 AF XY: 0.732 AC XY: 54428 AN XY: 74320

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.740

Alfa AF: 0.707 Hom.: 39132

Bravo AF: 0.749

Asia WGS AF: 0.669 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321000; hg19: chr20-44801026;