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. The variant received -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
• Publications: 19 publications found

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507166.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-47137G>A		intron	N/A	ENSP00000423325.1	A0A0B4J203

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

African (AFR) AF: 0.608 AC: 25140 AN: 41370

American (AMR) AF: 0.401 AC: 6121 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1487 AN: 5134

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4818

European-Finnish (FIN) AF: 0.271 AC: 2856 AN: 10528

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18800 AN: 67942

Other (OTH) AF: 0.333 AC: 699 AN: 2100

Alfa AF: 0.314 Hom.: 23577

Bravo AF: 0.399

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.96
PhyloP100		2.9
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6554162;

hg19: chr4-55093955;