rs4141626

Positions:

• chr20-4563547-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 0.866 in 152,170 control chromosomes in the GnomAD database, including 57,683 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 0.87 (57683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.927 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: 0.866 AC: 131650 AN: 152052 Hom.: 57672 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.866 AC: 131707 AN: 152170 Hom.: 57683 Cov.: 32 AF XY: 0.872 AC XY: 64832 AN XY: 74388

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.870

Alfa AF: 0.901 Hom.: 13101

Bravo AF: 0.852

Asia WGS AF: 0.907 AC: 3152 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4141626; hg19: chr20-4544193;