rs8111948

chr19-28334588-A-G

Variant summary

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

The ENST00000592311.5(ENSG00000267320):n.251-14330T>C 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 0.39 in 152,016 control chromosomes in the GnomAD database, including 13,782 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 0.39 (13782 hom., cov: 32)
• Consequence: ENST00000592311.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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
	ENST00000592311.5	n.251-14330T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000587140.5	n.530-1759T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59233 AN: 151898 Hom.: 13781 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.390 AC: 59240 AN: 152016 Hom.: 13782 Cov.: 32 AF XY: 0.398 AC XY: 29567 AN XY: 74316

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.402

Alfa AF: 0.422 Hom.: 3983

Bravo AF: 0.361

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8111948; hg19: chr19-28825495;