rs6554162

Variant names:

• chr4-54227788-G-A
• rs6554162
• ENST00000507166.5:c.1018-47137G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-54227788-G-A
• chr4-54227788-G-C

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-47137G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.93

Genes affected

ENSG00000282278 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-47137G>A		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

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;