rs300555

Variant names:

• chr4-123382130-G-A
• rs300555

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;