chr19-39944141-T-C

Position:

• chr19-39944141-T-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 0.277 in 151,944 control chromosomes in the GnomAD database, including 10,841 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 0.28 (10841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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: 0.277 AC: 41992 AN: 151828 Hom.: 10794 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.277 AC: 42103 AN: 151944 Hom.: 10841 Cov.: 32 AF XY: 0.275 AC XY: 20404 AN XY: 74266

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0908

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.239

Alfa AF: 0.162 Hom.: 2405

Bravo AF: 0.297

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2231738; hg19: chr19-40450048;