rs714392

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000223838 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000223838	ENST00000779060.1	n.83-7003A>G		intron_variant	Intron 1 of 1
ENSG00000223838	ENST00000779061.1	n.237-7003A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.563 AC: 23334 AN: 41436

American (AMR) AF: 0.509 AC: 7745 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2315 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1135 AN: 5160

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4812

European-Finnish (FIN) AF: 0.714 AC: 7547 AN: 10574

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43468 AN: 67854

Other (OTH) AF: 0.582 AC: 1225 AN: 2104

Alfa AF: 0.619 Hom.: 32526

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs714392; hg19: chr7-19611149;