3-19638916-C-T

Position:

• chr3-19638916-C-T

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 0.185 in 151,904 control chromosomes in the GnomAD database, including 4,052 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 (4052 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.19638916C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287069	ENST00000670571.1	n.512-22863G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28037 AN: 151786 Hom.: 4040 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.185 AC: 28095 AN: 151904 Hom.: 4052 Cov.: 32 AF XY: 0.185 AC XY: 13704 AN XY: 74250

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.175

Alfa AF: 0.103 Hom.: 604

Bravo AF: 0.204

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203428; hg19: chr3-19680408;