rs739495

Variant names:

• chr19-35171906-A-C
• rs739495

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 0.257 in 149,566 control chromosomes in the GnomAD database, including 7,006 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 0.26 (7006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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: 0.257 AC: 38364 AN: 149450 Hom.: 6994 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.257 AC: 38412 AN: 149566 Hom.: 7006 Cov.: 31 AF XY: 0.259 AC XY: 18930 AN XY: 72964

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.275

Alfa AF: 0.293 Hom.: 2567

Asia WGS AF: 0.394 AC: 1322 AN: 3358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739495; hg19: chr19-35662809;