rs10034719

Positions:

• chr4-16158651-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 0.376 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;