20-4437510-T-C

Variant names:

• chr20-4437510-T-C
• rs6037842

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 0.0687 in 152,174 control chromosomes in the GnomAD database, including 883 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 0.069 (883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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: 0.0685 AC: 10411 AN: 152056 Hom.: 875 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0917

Gnomad FIN AF: 0.00320

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0687 AC: 10455 AN: 152174 Hom.: 883 Cov.: 32 AF XY: 0.0686 AC XY: 5102 AN XY: 74420

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0419

Gnomad4 ASJ AF: 0.0449

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0914

Gnomad4 FIN AF: 0.00320

Gnomad4 NFE AF: 0.0124

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0375 Hom.: 124

Bravo AF: 0.0754

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6037842; hg19: chr20-4418157;