rs436681

Positions:

• chr19-43681774-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 0.875 in 152,208 control chromosomes in the GnomAD database, including 58,919 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 (58919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133039 AN: 152090 Hom.: 58879 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.875 AC: 133133 AN: 152208 Hom.: 58919 Cov.: 32 AF XY: 0.867 AC XY: 64509 AN XY: 74412

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.869

Alfa AF: 0.888 Hom.: 115870

Bravo AF: 0.861

Asia WGS AF: 0.668 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs436681; hg19: chr19-44185926;