4-89854061-A-G

Position:

• chr4-89854061-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.325 in 152,124 control chromosomes in the GnomAD database, including 8,622 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 0.33 (8622 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49446 AN: 152002 Hom.: 8625 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.325 AC: 49445 AN: 152124 Hom.: 8622 Cov.: 33 AF XY: 0.322 AC XY: 23951 AN XY: 74338

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.300

Alfa AF: 0.374 Hom.: 13364

Bravo AF: 0.310

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516848; hg19: chr4-90775212;