4-10164155-G-T

Variant names:

• chr4-10164155-G-T
• rs16894270

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.345 AC: 14314 AN: 41476

American (AMR) AF: 0.272 AC: 4154 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1177 AN: 5164

South Asian (SAS) AF: 0.380 AC: 1836 AN: 4826

European-Finnish (FIN) AF: 0.315 AC: 3338 AN: 10586

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.313 AC: 21242 AN: 67970

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.310 Hom.: 31560

Bravo AF: 0.309

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.58
DANN	Benign	0.45
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs16894270; hg19: chr4-10165779;