rs1329656

Positions:

• chr10-91593199-A-T

Variant summary

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

The NR_024467.1(HECTD2-AS1):​n.110+18152T>A 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 0.345 in 152,180 control chromosomes in the GnomAD database, including 9,402 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 0.34 (9402 hom., cov: 33)
• Consequence: HECTD2-AS1 NR_024467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

HECTD2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.110+18152T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52420 AN: 152060 Hom.: 9397 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.345 AC: 52469 AN: 152180 Hom.: 9402 Cov.: 33 AF XY: 0.334 AC XY: 24869 AN XY: 74412

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.386

Alfa AF: 0.361 Hom.: 1229

Bravo AF: 0.353

Asia WGS AF: 0.241 AC: 838 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	1.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1329656; hg19: chr10-93352956;