chr4-89845944-A-C

Position:

• chr4-89845944-A-C

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 0.186 in 151,848 control chromosomes in the GnomAD database, including 3,327 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 0.19 (3327 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.186 AC: 28275 AN: 151732 Hom.: 3325 Cov.: 30

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.186 AC: 28290 AN: 151848 Hom.: 3327 Cov.: 30 AF XY: 0.184 AC XY: 13650 AN XY: 74212

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.205

Alfa AF: 0.117 Hom.: 248

Bravo AF: 0.179

Asia WGS AF: 0.0610 AC: 214 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2619367; hg19: chr4-90767095;