rs10509626

chr10-91558639-A-G

Variant summary

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

The NR_024467.1(HECTD2-AS1):n.111-19061T>C 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 0.0558 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 NR_024467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.111-19061T>C		intron_variant, non_coding_transcript_variant
LOC105378433	XR_007062244.1	n.278+1895A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688440.1	n.199+16406T>C		intron_variant, non_coding_transcript_variant
	ENST00000700888.1	n.96+16406T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.00981

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.00507

Gnomad4 OTH AF: 0.0369

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509626; hg19: chr10-93318396;