rs4622984

Variant names:

• chr4-154531081-T-C
• rs4622984

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 0.604 in 151,892 control chromosomes in the GnomAD database, including 28,171 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 0.60 (28171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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: 0.604 AC: 91717 AN: 151776 Hom.: 28158 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.604 AC: 91766 AN: 151892 Hom.: 28171 Cov.: 31 AF XY: 0.599 AC XY: 44475 AN XY: 74260

African (AFR) AF: 0.524 AC: 21711 AN: 41442

American (AMR) AF: 0.632 AC: 9647 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2149 AN: 5182

South Asian (SAS) AF: 0.634 AC: 3050 AN: 4810

European-Finnish (FIN) AF: 0.566 AC: 5939 AN: 10486

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45081 AN: 67924

Other (OTH) AF: 0.642 AC: 1353 AN: 2108

Alfa AF: 0.657 Hom.: 51353

Bravo AF: 0.605

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.48
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs4622984; hg19: chr4-155452233;