19-12821455-G-A

Variant names:

• chr19-12821455-G-A
• rs7255045
• ENST00000589765.1:n.41+3723C>T

Variant summary

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

The ENST00000589765.1(HOOK2):​n.41+3723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,732 control chromosomes in the GnomAD database, including 11,489 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 0.37 (11489 hom., cov: 31)
• Consequence: HOOK2 ENST00000589765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 30 publications found

Genes affected

HOOK2 (HGNC:19885): (hook microtubule tethering protein 2) Hook proteins are cytosolic coiled-coil proteins that contain conserved N-terminal domains, which attach to microtubules, and more divergent C-terminal domains, which mediate binding to organelles. The Drosophila Hook protein is a component of the endocytic compartment.[supplied by OMIM, Apr 2004]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589765.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOOK2	ENST00000589765.1	TSL:5	n.41+3723C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55827 AN: 151614 Hom.: 11472 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.368 AC: 55889 AN: 151732 Hom.: 11489 Cov.: 31 AF XY: 0.376 AC XY: 27839 AN XY: 74136

African (AFR) AF: 0.531 AC: 21950 AN: 41352

American (AMR) AF: 0.359 AC: 5463 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2731 AN: 5150

South Asian (SAS) AF: 0.480 AC: 2312 AN: 4818

European-Finnish (FIN) AF: 0.345 AC: 3628 AN: 10510

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18216 AN: 67912

Other (OTH) AF: 0.305 AC: 642 AN: 2106

Alfa AF: 0.330 Hom.: 1096

Bravo AF: 0.370

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.18
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7255045; hg19: chr19-12932269;