19-19362636-T-C

Variant names:

• chr19-19362636-T-C
• rs2905424
• ENST00000724943.1:n.383-3675A>G

Variant summary

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

The ENST00000724943.1(ENSG00000294647):​n.383-3675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,760 control chromosomes in the GnomAD database, including 26,124 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 0.57 (26124 hom., cov: 30)
• Consequence: ENSG00000294647 ENST00000724943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 31 publications found

Genes affected

ENSG00000294647 (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 (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904656	XR_007067161.1	n.119-3675A>G		intron_variant	Intron 1 of 1
LOC124904656	XR_007067162.1	n.93+45A>G		intron_variant	Intron 1 of 1
LOC124904656	XR_007067163.1	n.482-3675A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294647	ENST00000724943.1	n.383-3675A>G		intron_variant	Intron 2 of 2
ENSG00000294647	ENST00000724944.1	n.256-3675A>G		intron_variant	Intron 1 of 1
ENSG00000294647	ENST00000724945.1	n.176+45A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86763 AN: 151642 Hom.: 26131 Cov.: 30

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.572 AC: 86755 AN: 151760 Hom.: 26124 Cov.: 30 AF XY: 0.574 AC XY: 42594 AN XY: 74170

African (AFR) AF: 0.376 AC: 15554 AN: 41318

American (AMR) AF: 0.576 AC: 8772 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2267 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3411 AN: 5122

South Asian (SAS) AF: 0.494 AC: 2377 AN: 4810

European-Finnish (FIN) AF: 0.759 AC: 8034 AN: 10580

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44489 AN: 67930

Other (OTH) AF: 0.566 AC: 1192 AN: 2106

Alfa AF: 0.618 Hom.: 51534

Bravo AF: 0.551

Asia WGS AF: 0.542 AC: 1885 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	0.77
DANN	Benign	0.21
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2905424; hg19: chr19-19473445;