4-176605104-T-C

Variant names:

• chr4-176605104-T-C
• rs921308

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 0.0819 in 152,248 control chromosomes in the GnomAD database, including 713 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 0.082 (713 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12438 AN: 152130 Hom.: 712 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0579

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

GnomAD4 genome AF: 0.0819 AC: 12473 AN: 152248 Hom.: 713 Cov.: 33 AF XY: 0.0819 AC XY: 6100 AN XY: 74438

African (AFR) AF: 0.163 AC: 6767 AN: 41518

American (AMR) AF: 0.0585 AC: 895 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.139 AC: 717 AN: 5166

South Asian (SAS) AF: 0.0735 AC: 355 AN: 4828

European-Finnish (FIN) AF: 0.0449 AC: 477 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2961 AN: 68022

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.0676 Hom.: 60

Bravo AF: 0.0864

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.52
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs921308; hg19: chr4-177526255;