19-28065377-C-T

Variant names:

• chr19-28065377-C-T
• rs8107007
• ENST00000586671.5:n.99+12C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586671.5(ENSG00000267509):​n.99+12C>T variant causes a intron 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: ENSG00000267509 ENST00000586671.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 4 publications found

Genes affected

ENSG00000267509 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267509	ENST00000586671.5	n.99+12C>T		intron_variant	Intron 1 of 3	4
ENSG00000267509	ENST00000590229.2	n.99+12C>T		intron_variant	Intron 1 of 4	4
ENSG00000267509	ENST00000722298.1	n.99+12C>T		intron_variant	Intron 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.218 AC: 9058 AN: 41506

American (AMR) AF: 0.0817 AC: 1250 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3472

East Asian (EAS) AF: 0.0753 AC: 391 AN: 5190

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10588

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4438 AN: 68006

Other (OTH) AF: 0.0855 AC: 181 AN: 2116

Alfa AF: 0.0811 Hom.: 1786

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs8107007; hg19: chr19-28556284;