19-49727070-C-G

Position:

• chr19-49727070-C-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 0.0916 in 151,952 control chromosomes in the GnomAD database, including 1,230 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 0.092 (1230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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 = 0.212 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: 0.0914 AC: 13882 AN: 151834 Hom.: 1224 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0916 AC: 13915 AN: 151952 Hom.: 1230 Cov.: 31 AF XY: 0.0916 AC XY: 6800 AN XY: 74258

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0652

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.0196

Gnomad4 OTH AF: 0.0831

Alfa AF: 0.0175 Hom.: 11

Bravo AF: 0.108

Asia WGS AF: 0.109 AC: 380 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	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102150; hg19: chr19-50230327;