rs2179357

chr20-46742445-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 0.397 in 151,914 control chromosomes in the GnomAD database, including 12,416 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 0.40 (12416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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: 0.397 AC: 60233 AN: 151794 Hom.: 12385 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.397 AC: 60318 AN: 151914 Hom.: 12416 Cov.: 31 AF XY: 0.405 AC XY: 30054 AN XY: 74278

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.406

Alfa AF: 0.383 Hom.: 1430

Bravo AF: 0.402

Asia WGS AF: 0.499 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.6
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2179357; hg19: chr20-45371084;