19-35178168-G-A

Position:

• chr19-35178168-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 0.805 in 152,142 control chromosomes in the GnomAD database, including 49,419 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 0.81 (49419 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 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: 0.805 AC: 122370 AN: 152024 Hom.: 49367 Cov.: 31

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.805 AC: 122485 AN: 152142 Hom.: 49419 Cov.: 31 AF XY: 0.803 AC XY: 59717 AN XY: 74384

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.784

Alfa AF: 0.785 Hom.: 47156

Bravo AF: 0.810

Asia WGS AF: 0.789 AC: 2746 AN: 3478

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	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4805110; hg19: chr19-35669071;