ENST00000504537.1:n.114+3168A>G

Variant names:

• chr4-59627043-T-C
• rs10866168
• ENST00000504537.1:n.114+3168A>G

Variant summary

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

The ENST00000504537.1(ENSG00000249392):​n.114+3168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,840 control chromosomes in the GnomAD database, including 30,157 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 0.62 (30157 hom., cov: 30)
• Consequence: ENSG00000249392 ENST00000504537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

Genes affected

ENSG00000249392 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249392	ENST00000504537.1	TSL:3	n.114+3168A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93612 AN: 151722 Hom.: 30157 Cov.: 30

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.617 AC: 93626 AN: 151840 Hom.: 30157 Cov.: 30 AF XY: 0.616 AC XY: 45736 AN XY: 74200

African (AFR) AF: 0.414 AC: 17138 AN: 41394

American (AMR) AF: 0.705 AC: 10736 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2373 AN: 3466

East Asian (EAS) AF: 0.657 AC: 3370 AN: 5130

South Asian (SAS) AF: 0.629 AC: 3022 AN: 4804

European-Finnish (FIN) AF: 0.661 AC: 6962 AN: 10536

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47880 AN: 67962

Other (OTH) AF: 0.630 AC: 1329 AN: 2108

Alfa AF: 0.665 Hom.: 13705

Bravo AF: 0.614

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10866168; hg19: chr4-60492761;