chr19-10381030-G-C

Position:

• chr19-10381030-G-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 0.0538 in 151,962 control chromosomes in the GnomAD database, including 266 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 0.054 (266 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0663 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: 0.0538 AC: 8171 AN: 151844 Hom.: 266 Cov.: 31

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0538 AC: 8175 AN: 151962 Hom.: 266 Cov.: 31 AF XY: 0.0529 AC XY: 3927 AN XY: 74302

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0600 Hom.: 42

Bravo AF: 0.0503

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12720214; hg19: chr19-10491706;