rs10857328

chr4-160290772-A-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 0.246 in 152,164 control chromosomes in the GnomAD database, including 5,360 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 0.25 (5360 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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: 0.246 AC: 37449 AN: 152046 Hom.: 5352 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.246 AC: 37479 AN: 152164 Hom.: 5360 Cov.: 33 AF XY: 0.248 AC XY: 18425 AN XY: 74384

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.256

Alfa AF: 0.285 Hom.: 858

Bravo AF: 0.244

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.11
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10857328; hg19: chr4-161211924;