rs4803381

chr19-40851439-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.569 in 138,240 control chromosomes in the GnomAD database, including 21,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.57 (21385 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 19-40851439-T-C is Benign according to our data. Variant chr19-40851439-T-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.623 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: 0.569 AC: 78637 AN: 138126 Hom.: 21370 Cov.: 25

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.578

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.569 AC: 78683 AN: 138240 Hom.: 21385 Cov.: 25 AF XY: 0.567 AC XY: 38158 AN XY: 67290

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.565

Alfa AF: 0.607 Hom.: 2967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803381; hg19: chr19-41357344;