20-48460486-A-G

Variant names:

• chr20-48460486-A-G
• rs910191

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 0.321 in 152,012 control chromosomes in the GnomAD database, including 8,335 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 0.32 (8335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 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: 0.321 AC: 48772 AN: 151894 Hom.: 8321 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.321 AC: 48815 AN: 152012 Hom.: 8335 Cov.: 32 AF XY: 0.330 AC XY: 24534 AN XY: 74300

African (AFR) AF: 0.263 AC: 10904 AN: 41460

American (AMR) AF: 0.468 AC: 7156 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2690 AN: 5160

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4820

European-Finnish (FIN) AF: 0.371 AC: 3918 AN: 10562

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20499 AN: 67938

Other (OTH) AF: 0.305 AC: 644 AN: 2114

Alfa AF: 0.315 Hom.: 15757

Bravo AF: 0.329

Asia WGS AF: 0.406 AC: 1411 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	2.1
DANN	Benign	0.72
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs910191; hg19: chr20-47088732;