rs714392

Variant names:

• chr7-19571526-A-G
• rs714392
• ENST00000412563.1:n.357-4761A>G

Variant summary

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

The ENST00000412563.1(ENSG00000223838):​n.357-4761A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,842 control chromosomes in the GnomAD database, including 27,108 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 0.59 (27108 hom., cov: 32)
• Consequence: ENSG00000223838 ENST00000412563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

Genes affected

ENSG00000223838 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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
ENSG00000223838	ENST00000412563.1	n.357-4761A>G		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89141 AN: 151724 Hom.: 27078 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.588 AC: 89215 AN: 151842 Hom.: 27108 Cov.: 32 AF XY: 0.580 AC XY: 43045 AN XY: 74184

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.582

Alfa AF: 0.620 Hom.: 27286

Bravo AF: 0.575

Asia WGS AF: 0.313 AC: 1091 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714392; hg19: chr7-19611149;