rs74676832

chr19-56171378-T-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 0.0425 in 152,278 control chromosomes in the GnomAD database, including 157 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 0.042 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0657 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: 0.0423 AC: 6433 AN: 152160 Hom.: 152 Cov.: 32

Gnomad AFR AF: 0.0673

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0394

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0425 AC: 6465 AN: 152278 Hom.: 157 Cov.: 32 AF XY: 0.0409 AC XY: 3045 AN XY: 74466

Gnomad4 AFR AF: 0.0678

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0178

Gnomad4 NFE AF: 0.0394

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0434 Hom.: 21

Bravo AF: 0.0433

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74676832; hg19: chr19-56682747;