rs1588041

Variant names:

• chr4-116225850-T-C
• rs1588041
• ENST00000508414.5:n.203-29113A>G

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.203-29113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,082 control chromosomes in the GnomAD database, including 41,913 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 0.68 (41913 hom., cov: 31)
• Consequence: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 publications found

Genes affected

ENSG00000293005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508414.5. 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
	ENSG00000293005	ENST00000508414.5	TSL:3	n.203-29113A>G		intron	N/A
	ENSG00000293005	ENST00000509983.2	TSL:3	n.265-29113A>G		intron	N/A
	ENSG00000293005	ENST00000775331.1		n.412-29113A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104086 AN: 151962 Hom.: 41914 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.684 AC: 104087 AN: 152082 Hom.: 41913 Cov.: 31 AF XY: 0.690 AC XY: 51300 AN XY: 74350

African (AFR) AF: 0.226 AC: 9374 AN: 41470

American (AMR) AF: 0.779 AC: 11888 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2837 AN: 3468

East Asian (EAS) AF: 0.899 AC: 4643 AN: 5162

South Asian (SAS) AF: 0.763 AC: 3674 AN: 4814

European-Finnish (FIN) AF: 0.921 AC: 9754 AN: 10596

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59339 AN: 67994

Other (OTH) AF: 0.700 AC: 1475 AN: 2108

Alfa AF: 0.828 Hom.: 53653

Bravo AF: 0.654

Asia WGS AF: 0.777 AC: 2698 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		0.15

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: rs1588041;

hg19: chr4-117147006;