chr19-28375689-G-A

Variant names:

• chr19-28375689-G-A
• rs995834
• ENST00000587140.5:n.193-313C>T

Variant summary

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

The ENST00000587140.5(ENSG00000267320):​n.193-313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,998 control chromosomes in the GnomAD database, including 31,035 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 0.62 (31035 hom., cov: 32)
• Consequence: ENSG00000267320 ENST00000587140.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 8 publications found

Genes affected

ENSG00000267320 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 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
ENSG00000267320	ENST00000587140.5	n.193-313C>T		intron_variant	Intron 2 of 4	5
ENSG00000267320	ENST00000591926.1	n.160-313C>T		intron_variant	Intron 2 of 3	4
ENSG00000267320	ENST00000592311.5	n.167-313C>T		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93939 AN: 151880 Hom.: 31027 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.618 AC: 93962 AN: 151998 Hom.: 31035 Cov.: 32 AF XY: 0.622 AC XY: 46225 AN XY: 74316

African (AFR) AF: 0.386 AC: 15963 AN: 41408

American (AMR) AF: 0.620 AC: 9463 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2569 AN: 5170

South Asian (SAS) AF: 0.652 AC: 3141 AN: 4814

European-Finnish (FIN) AF: 0.775 AC: 8202 AN: 10580

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49934 AN: 67964

Other (OTH) AF: 0.637 AC: 1346 AN: 2112

Alfa AF: 0.684 Hom.: 106662

Bravo AF: 0.594

Asia WGS AF: 0.533 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.45
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs995834; hg19: chr19-28866596;