rs735842

chr19-4007082-T-Cchr19-4007082-T-G

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 0.212 in 148,982 control chromosomes in the GnomAD database, including 3,576 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 0.21 (3576 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.212 AC: 31585 AN: 148858 Hom.: 3577 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.212 AC: 31594 AN: 148982 Hom.: 3576 Cov.: 31 AF XY: 0.211 AC XY: 15332 AN XY: 72654

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0261

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.224

Alfa AF: 0.191 Hom.: 4578

Bravo AF: 0.210

Asia WGS AF: 0.0980 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.063
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735842; hg19: chr19-4007080;