chr19-39240115-A-T

Variant names:

• chr19-39240115-A-T
• rs35790907

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 0.396 in 151,772 control chromosomes in the GnomAD database, including 14,179 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 0.40 (14179 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59945 AN: 151654 Hom.: 14147 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.396 AC: 60032 AN: 151772 Hom.: 14179 Cov.: 31 AF XY: 0.387 AC XY: 28711 AN XY: 74196

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.368

Alfa AF: 0.351 Hom.: 1267

Bravo AF: 0.419

Asia WGS AF: 0.203 AC: 710 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	0.66
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35790907; hg19: chr19-39730755;