rs2018964

chr4-155386292-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 0.0976 in 152,106 control chromosomes in the GnomAD database, including 1,727 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 0.098 (1727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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 (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.0974 AC: 14809 AN: 151988 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0976 AC: 14850 AN: 152106 Hom.: 1727 Cov.: 32 AF XY: 0.0959 AC XY: 7129 AN XY: 74368

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0454

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.00754

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0641 Hom.: 163

Bravo AF: 0.109

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2018964; hg19: chr4-156307444;