rs300555

chr4-123382130-G-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 0.589 in 151,774 control chromosomes in the GnomAD database, including 27,029 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 0.59 (27029 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 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: 0.589 AC: 89325 AN: 151656 Hom.: 27018 Cov.: 30

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.589 AC: 89369 AN: 151774 Hom.: 27029 Cov.: 30 AF XY: 0.585 AC XY: 43401 AN XY: 74160

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.594

Alfa AF: 0.639 Hom.: 40784

Bravo AF: 0.576

Asia WGS AF: 0.414 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs300555; hg19: chr4-124303285;