rs6554162

chr4-54227788-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.378 in 151,824 control chromosomes in the GnomAD database, including 12,466 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 0.38 (12466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.93

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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: 0.377 AC: 57264 AN: 151706 Hom.: 12421 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.378 AC: 57368 AN: 151824 Hom.: 12466 Cov.: 31 AF XY: 0.375 AC XY: 27849 AN XY: 74200

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.333

Alfa AF: 0.291 Hom.: 11730

Bravo AF: 0.399

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
Cadd	Benign	17
Dann	Benign	0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6554162; hg19: chr4-55093955;