4-154616169-G-A

Variant names:

• chr4-154616169-G-A
• rs12644950

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 0.257 in 151,974 control chromosomes in the GnomAD database, including 5,264 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 0.26 (5264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38958 AN: 151856 Hom.: 5256 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.257 AC: 38996 AN: 151974 Hom.: 5264 Cov.: 32 AF XY: 0.259 AC XY: 19273 AN XY: 74280

African (AFR) AF: 0.266 AC: 11004 AN: 41404

American (AMR) AF: 0.218 AC: 3330 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 494 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2327 AN: 5162

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4820

European-Finnish (FIN) AF: 0.306 AC: 3226 AN: 10556

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16454 AN: 67978

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.234 Hom.: 5807

Bravo AF: 0.252

Asia WGS AF: 0.320 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12644950; hg19: chr4-155537321;