chr4-148728881-G-A

Variant names:

• chr4-148728881-G-A
• rs17025017
• ENST00000661928.1:n.223-137876G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661928.1(ENSG00000287292):​n.223-137876G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,074 control chromosomes in the GnomAD database, including 5,721 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 0.25 (5721 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 6 publications found

Genes affected

ENSG00000287292 (HGNC:58892):

LOC107986195 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.223-137876G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37822 AN: 151956 Hom.: 5717 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37854 AN: 152074 Hom.: 5721 Cov.: 32 AF XY: 0.241 AC XY: 17897 AN XY: 74348

African (AFR) AF: 0.427 AC: 17694 AN: 41448

American (AMR) AF: 0.174 AC: 2663 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3470

East Asian (EAS) AF: 0.0626 AC: 324 AN: 5176

South Asian (SAS) AF: 0.151 AC: 728 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1231 AN: 10588

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13819 AN: 67972

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.217 Hom.: 12925

Bravo AF: 0.263

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.18

Splicing

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: rs17025017;

hg19: chr4-149650033;