10-91558639-A-G

Variant names:

• chr10-91558639-A-G
• rs10509626
• ENST00000688440.2:n.246+16406T>C

Variant summary

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

The ENST00000688440.2(HECTD2-AS1):​n.246+16406T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,128 control chromosomes in the GnomAD database, including 742 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 0.056 (742 hom., cov: 31)
• Consequence: HECTD2-AS1 ENST00000688440.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 0 publications found

Genes affected

HECTD2-AS1 (HGNC:):

HECTD2-AS1 (HGNC:48679): (HECTD2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HECTD2-AS1	NR_024467.1	n.111-19061T>C		intron_variant	Intron 1 of 4
LOC105378433	XR_007062244.1	n.278+1895A>G		intron_variant	Intron 2 of 2
LOC105378433	XR_001747548.3	n.*206A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HECTD2-AS1	ENST00000688440.2	n.246+16406T>C		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000700888.2	n.96+16406T>C		intron_variant	Intron 2 of 4
HECTD2-AS1	ENST00000838016.1	n.167-33490T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8451 AN: 152010 Hom.: 736 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.00981

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00507

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0558 AC: 8488 AN: 152128 Hom.: 742 Cov.: 31 AF XY: 0.0545 AC XY: 4050 AN XY: 74374

African (AFR) AF: 0.183 AC: 7581 AN: 41454

American (AMR) AF: 0.0251 AC: 383 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00981 AC: 34 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4818

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00507 AC: 345 AN: 68008

Other (OTH) AF: 0.0369 AC: 78 AN: 2114

Alfa AF: 0.0332 Hom.: 51

Bravo AF: 0.0633

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.83
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10509626; hg19: chr10-93318396;