chr4-122551631-A-G

Variant names:

• chr4-122551631-A-G
• rs4572894

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 0.215 in 152,138 control chromosomes in the GnomAD database, including 3,894 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 0.22 (3894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 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: 0.215 AC: 32741 AN: 152018 Hom.: 3894 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.215 AC: 32750 AN: 152138 Hom.: 3894 Cov.: 32 AF XY: 0.207 AC XY: 15374 AN XY: 74364

African (AFR) AF: 0.147 AC: 6121 AN: 41526

American (AMR) AF: 0.190 AC: 2902 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3470

East Asian (EAS) AF: 0.138 AC: 713 AN: 5180

South Asian (SAS) AF: 0.163 AC: 785 AN: 4816

European-Finnish (FIN) AF: 0.140 AC: 1484 AN: 10586

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18791 AN: 67980

Other (OTH) AF: 0.231 AC: 486 AN: 2106

Alfa AF: 0.220 Hom.: 693

Bravo AF: 0.217

Asia WGS AF: 0.167 AC: 582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.74
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs4572894; hg19: chr4-123472786;