rs8107007

Positions:

• chr19-28065377-C-T

Variant summary

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

The ENST00000590229.1(ENSG00000267509):​n.99+12C>T 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 0.112 in 152,202 control chromosomes in the GnomAD database, including 1,324 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 0.11 (1324 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENST00000590229.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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
	ENST00000590229.1	n.99+12C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000586671.5	n.99+12C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17014 AN: 152084 Hom.: 1322 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.0840

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.112 AC: 17045 AN: 152202 Hom.: 1324 Cov.: 33 AF XY: 0.112 AC XY: 8317 AN XY: 74422

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.0753

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0704 Hom.: 454

Bravo AF: 0.114

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8107007; hg19: chr19-28556284;