rs4810624

Positions:

• chr20-37414503-T-C

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 0.0454 in 150,556 control chromosomes in the GnomAD database, including 278 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 0.045 (278 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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 (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0453 AC: 6819 AN: 150434 Hom.: 280 Cov.: 27

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0355

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0454 AC: 6830 AN: 150556 Hom.: 278 Cov.: 27 AF XY: 0.0465 AC XY: 3415 AN XY: 73492

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0511

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0182

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0372 Hom.: 76

Bravo AF: 0.0536

Asia WGS AF: 0.107 AC: 370 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	12
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810624; hg19: chr20-36042906;