rs732841

Positions:

• chr19-45704552-A-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 0.0669 in 152,140 control chromosomes in the GnomAD database, including 457 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 0.067 (457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0669 AC: 10174 AN: 152022 Hom.: 455 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0669 AC: 10179 AN: 152140 Hom.: 457 Cov.: 32 AF XY: 0.0654 AC XY: 4864 AN XY: 74362

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0337

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.0975

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.0579

Alfa AF: 0.0512 Hom.: 334

Bravo AF: 0.0665

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
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: rs732841; hg19: chr19-46207810;