4-188819384-C-T

Variant names:

• chr4-188819384-C-T
• rs10032223

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 0.172 in 152,126 control chromosomes in the GnomAD database, including 2,392 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 0.17 (2392 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 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: 0.172 AC: 26094 AN: 152006 Hom.: 2388 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.172 AC: 26122 AN: 152126 Hom.: 2392 Cov.: 33 AF XY: 0.166 AC XY: 12367 AN XY: 74364

African (AFR) AF: 0.139 AC: 5752 AN: 41512

American (AMR) AF: 0.127 AC: 1942 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 873 AN: 3472

East Asian (EAS) AF: 0.0421 AC: 218 AN: 5178

South Asian (SAS) AF: 0.162 AC: 779 AN: 4822

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10578

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13965 AN: 67962

Other (OTH) AF: 0.170 AC: 360 AN: 2112

Alfa AF: 0.0922 Hom.: 139

Bravo AF: 0.164

Asia WGS AF: 0.123 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.51
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs10032223; hg19: chr4-189740538;