rs12188464

Variant names:

• chr5-68668122-A-G
• rs12188464
• ENST00000688207.1:n.66-50607T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688207.1(ENSG00000250237):​n.66-50607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,006 control chromosomes in the GnomAD database, including 38,966 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 0.70 (38966 hom., cov: 31)
• Consequence: ENSG00000250237 ENST00000688207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

Genes affected

ENSG00000250237 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.441-50607T>C		intron_variant	Intron 2 of 4
LOC105379013	XR_007058805.1	n.111-50607T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250237	ENST00000688207.1	n.66-50607T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106444 AN: 151888 Hom.: 38965 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.700 AC: 106477 AN: 152006 Hom.: 38966 Cov.: 31 AF XY: 0.697 AC XY: 51809 AN XY: 74296

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.717

Alfa AF: 0.791 Hom.: 21705

Bravo AF: 0.669

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12188464; hg19: chr5-67963949;