rs436681

Variant names:

• chr19-43681774-G-A
• rs436681

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.929 AC: 38571 AN: 41536

American (AMR) AF: 0.728 AC: 11111 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3191 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2682 AN: 5176

South Asian (SAS) AF: 0.755 AC: 3639 AN: 4820

European-Finnish (FIN) AF: 0.890 AC: 9432 AN: 10598

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61546 AN: 68026

Other (OTH) AF: 0.869 AC: 1832 AN: 2108

Alfa AF: 0.887 Hom.: 247991

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs436681; hg19: chr19-44185926;