14-49067707-G-C

Variant names:

• chr14-49067707-G-C
• rs8013477
• ENST00000557062.1:n.284+2085C>G

Variant summary

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

The ENST00000557062.1(ENSG00000258868):​n.284+2085C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 150,914 control chromosomes in the GnomAD database, including 4,657 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 0.22 (4657 hom., cov: 30)
• Consequence: ENSG00000258868 ENST00000557062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 publications found

Genes affected

ENSG00000258868 (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 = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557062.1. 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
	ENSG00000258868	ENST00000557062.1	TSL:3	n.284+2085C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33651 AN: 150786 Hom.: 4652 Cov.: 30

Gnomad AFR AF: 0.0711

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.223 AC: 33660 AN: 150914 Hom.: 4657 Cov.: 30 AF XY: 0.227 AC XY: 16733 AN XY: 73668

African (AFR) AF: 0.0711 AC: 2926 AN: 41172

American (AMR) AF: 0.320 AC: 4844 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2403 AN: 5050

South Asian (SAS) AF: 0.412 AC: 1949 AN: 4730

European-Finnish (FIN) AF: 0.204 AC: 2104 AN: 10304

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17668 AN: 67764

Other (OTH) AF: 0.265 AC: 554 AN: 2088

Alfa AF: 0.268 Hom.: 3283

Bravo AF: 0.225

Asia WGS AF: 0.445 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		0.36

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: rs8013477;

hg19: chr14-49534425;