chr4-10164155-G-T

Variant names:

• chr4-10164155-G-T
• rs16894270

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 0.315 in 152,100 control chromosomes in the GnomAD database, including 7,598 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 0.31 (7598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 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: 0.315 AC: 47856 AN: 151982 Hom.: 7599 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.315 AC: 47882 AN: 152100 Hom.: 7598 Cov.: 32 AF XY: 0.315 AC XY: 23416 AN XY: 74346

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.302

Alfa AF: 0.305 Hom.: 14900

Bravo AF: 0.309

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.58
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16894270; hg19: chr4-10165779;