rs10866168

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000249392 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000249392	ENST00000504537.1	n.114+3168A>G		intron_variant	Intron 1 of 5	3

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

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.630

Alfa AF: 0.665 Hom.: 8800

Bravo AF: 0.614

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10866168; hg19: chr4-60492761;