rs2207418

Positions:

• chr20-11194255-G-A

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 0.732 in 152,122 control chromosomes in the GnomAD database, including 41,677 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 0.73 (41677 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.732 AC: 111252 AN: 152004 Hom.: 41620 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.732 AC: 111361 AN: 152122 Hom.: 41677 Cov.: 33 AF XY: 0.724 AC XY: 53823 AN XY: 74344

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.723

Alfa AF: 0.724 Hom.: 56369

Bravo AF: 0.721

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207418; hg19: chr20-11174903;