rs10034719

Variant names:

• chr4-16158651-C-T
• rs10034719

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 0.376 in 152,062 control chromosomes in the GnomAD database, including 11,149 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 0.38 (11149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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: 0.375 AC: 57049 AN: 151944 Hom.: 11121 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.376 AC: 57117 AN: 152062 Hom.: 11149 Cov.: 32 AF XY: 0.369 AC XY: 27444 AN XY: 74330

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.379

Alfa AF: 0.355 Hom.: 3270

Bravo AF: 0.378

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
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: rs10034719; hg19: chr4-16160274;