4-178960633-T-C

Variant names:

• chr4-178960633-T-C
• rs1075182

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 0.305 in 152,064 control chromosomes in the GnomAD database, including 7,277 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 0.30 (7277 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.305 AC: 46288 AN: 151946 Hom.: 7270 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.305 AC: 46328 AN: 152064 Hom.: 7277 Cov.: 31 AF XY: 0.300 AC XY: 22327 AN XY: 74336

African (AFR) AF: 0.287 AC: 11881 AN: 41466

American (AMR) AF: 0.217 AC: 3316 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1295 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5160

South Asian (SAS) AF: 0.212 AC: 1025 AN: 4824

European-Finnish (FIN) AF: 0.307 AC: 3240 AN: 10566

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23247 AN: 67982

Other (OTH) AF: 0.322 AC: 682 AN: 2116

Alfa AF: 0.324 Hom.: 1339

Bravo AF: 0.298

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1075182; hg19: chr4-179881787;