4-89337437-T-G

Variant names:

• chr4-89337437-T-G
• rs1504489

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 0.481 in 152,054 control chromosomes in the GnomAD database, including 19,155 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 0.48 (19155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 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: 0.481 AC: 73080 AN: 151938 Hom.: 19163 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.481 AC: 73078 AN: 152054 Hom.: 19155 Cov.: 32 AF XY: 0.479 AC XY: 35614 AN XY: 74324

African (AFR) AF: 0.273 AC: 11342 AN: 41498

American (AMR) AF: 0.447 AC: 6827 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2166 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5162

South Asian (SAS) AF: 0.508 AC: 2444 AN: 4812

European-Finnish (FIN) AF: 0.583 AC: 6161 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40854 AN: 67962

Other (OTH) AF: 0.486 AC: 1024 AN: 2108

Alfa AF: 0.557 Hom.: 13041

Bravo AF: 0.457

Asia WGS AF: 0.369 AC: 1289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1504489; hg19: chr4-90258588; COSMIC: COSV56536973;