19-39241264-T-C

Position:

• chr19-39241264-T-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 0.317 in 151,856 control chromosomes in the GnomAD database, including 8,013 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 0.32 (8013 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39241264T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48103 AN: 151738 Hom.: 8005 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.317 AC: 48146 AN: 151856 Hom.: 8013 Cov.: 31 AF XY: 0.310 AC XY: 23021 AN XY: 74220

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.0871

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.315

Alfa AF: 0.323 Hom.: 1001

Bravo AF: 0.333

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
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: rs12982533; hg19: chr19-39731904;