20-18940230-T-C

Variant names:

• chr20-18940230-T-C
• rs6105992

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 0.577 in 152,054 control chromosomes in the GnomAD database, including 25,457 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 0.58 (25457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.577 AC: 87647 AN: 151936 Hom.: 25445 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.577 AC: 87706 AN: 152054 Hom.: 25457 Cov.: 32 AF XY: 0.577 AC XY: 42876 AN XY: 74338

African (AFR) AF: 0.584 AC: 24219 AN: 41444

American (AMR) AF: 0.590 AC: 9020 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3820 AN: 5186

South Asian (SAS) AF: 0.645 AC: 3106 AN: 4818

European-Finnish (FIN) AF: 0.536 AC: 5666 AN: 10570

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38069 AN: 67966

Other (OTH) AF: 0.575 AC: 1213 AN: 2110

Alfa AF: 0.575 Hom.: 3159

Bravo AF: 0.581

Asia WGS AF: 0.651 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6105992; hg19: chr20-18920874;