14-60589222-A-G

Variant names:

• chr14-60589222-A-G
• rs10148202
• ENST00000827601.1:n.468-13930T>C

Variant summary

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

The ENST00000827601.1(ENSG00000307639):​n.468-13930T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,182 control chromosomes in the GnomAD database, including 60,852 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 0.89 (60852 hom., cov: 31)
• Consequence: ENSG00000307639 ENST00000827601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 6 publications found

Genes affected

ENSG00000307639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827601.1. 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
	ENSG00000307639	ENST00000827601.1		n.468-13930T>C		intron	N/A
	ENSG00000307639	ENST00000827602.1		n.405-13930T>C		intron	N/A
	ENSG00000307639	ENST00000827603.1		n.498-13930T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135706 AN: 152062 Hom.: 60794 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.893 AC: 135827 AN: 152182 Hom.: 60852 Cov.: 31 AF XY: 0.891 AC XY: 66305 AN XY: 74402

African (AFR) AF: 0.846 AC: 35108 AN: 41492

American (AMR) AF: 0.916 AC: 14003 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3115 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4042 AN: 5174

South Asian (SAS) AF: 0.731 AC: 3523 AN: 4818

European-Finnish (FIN) AF: 0.975 AC: 10347 AN: 10612

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62688 AN: 68014

Other (OTH) AF: 0.894 AC: 1889 AN: 2112

Alfa AF: 0.916 Hom.: 10794

Bravo AF: 0.888

Asia WGS AF: 0.790 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.56
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10148202; hg19: chr14-61055940;