19-40990556-T-C

Variant names:

• chr19-40990556-T-C
• rs4802101

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 0.698 in 151,420 control chromosomes in the GnomAD database, including 38,381 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 0.70 (38381 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 19-40990556-T-C is Benign according to our data. Variant chr19-40990556-T-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105547 AN: 151302 Hom.: 38331 Cov.: 28

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.698 AC: 105656 AN: 151420 Hom.: 38381 Cov.: 28 AF XY: 0.700 AC XY: 51735 AN XY: 73918

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.689

Alfa AF: 0.646 Hom.: 4115

Bravo AF: 0.717

Asia WGS AF: 0.713 AC: 2476 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802101; hg19: chr19-41496461;