chr4-160290772-A-T

Variant names:

• chr4-160290772-A-T
• rs10857328

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;