rs714392

chr7-19571526-A-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, non coding transcript 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: ENST00000412563.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412563.1	n.357-4761A>G		intron_variant, non_coding_transcript_variant		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;