chr19-49501100-G-A

Position:

• chr19-49501100-G-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 0.183 in 152,150 control chromosomes in the GnomAD database, including 3,663 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 0.18 (3663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27760 AN: 152032 Hom.: 3655 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.167

GnomAD3 exomes AF: 0.114 AC: 91 AN: 800 Hom.: 8 AF XY: 0.105 AC XY: 47 AN XY: 448

Gnomad AFR exome AF: 0.389

Gnomad AMR exome AF: 0.0604

Gnomad ASJ exome AF: 0.300

Gnomad EAS exome AF: 0.0208

Gnomad SAS exome AF: 0.102

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.100

Gnomad OTH exome AF: 0.0909

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

GnomAD4 genome AF: 0.183 AC: 27802 AN: 152150 Hom.: 3663 Cov.: 32 AF XY: 0.179 AC XY: 13299 AN XY: 74378

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.167

Alfa AF: 0.157 Hom.: 572

Bravo AF: 0.194

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.64

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: rs73056059; hg19: chr19-50004357;