14-49067707-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000258868 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378178	XR_007064152.1	n.345+2085C>G		intron_variant	Intron 4 of 9
LOC105378178	XR_007064153.1	n.345+2085C>G		intron_variant	Intron 4 of 4
LOC105378178	XR_943837.3	n.345+2085C>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258868	ENST00000557062.1	n.284+2085C>G		intron_variant	Intron 3 of 3	3

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

Gnomad4 AFR AF: 0.0711

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.265

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8013477; hg19: chr14-49534425;