chr4-89847220-C-A

Position:

• chr4-89847220-C-A

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 0.306 in 151,952 control chromosomes in the GnomAD database, including 8,048 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 0.31 (8048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46467 AN: 151834 Hom.: 8053 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46455 AN: 151952 Hom.: 8048 Cov.: 32 AF XY: 0.304 AC XY: 22561 AN XY: 74274

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.280

Alfa AF: 0.363 Hom.: 2875

Bravo AF: 0.287

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.59
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7678651; hg19: chr4-90768371;