chr20-37423443-C-T

Variant names:

• chr20-37423443-C-T
• rs6018432

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 0.211 in 152,066 control chromosomes in the GnomAD database, including 5,540 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 0.21 (5540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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: 0.210 AC: 31971 AN: 151948 Hom.: 5521 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.211 AC: 32048 AN: 152066 Hom.: 5540 Cov.: 32 AF XY: 0.203 AC XY: 15124 AN XY: 74380

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0212

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.181

Alfa AF: 0.145 Hom.: 1351

Bravo AF: 0.226

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6018432; hg19: chr20-36051846;