rs12247672

chr10-91404172-G-A

Variant summary

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

The NR_024467.1(HECTD2-AS1):n.427-53293C>T 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 0.177 in 152,158 control chromosomes in the GnomAD database, including 5,493 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 0.18 (5493 hom., cov: 32)
• Consequence: HECTD2-AS1 NR_024467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.427-53293C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688440.1	n.322-53293C>T		intron_variant, non_coding_transcript_variant
	ENST00000700888.1	n.219-53293C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26825 AN: 152040 Hom.: 5478 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.177 AC: 26875 AN: 152158 Hom.: 5493 Cov.: 32 AF XY: 0.172 AC XY: 12817 AN XY: 74408

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.0954

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0476

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0658 Hom.: 1443

Bravo AF: 0.194

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12247672; hg19: chr10-93163929;