rs12247672

Variant names:

• chr10-91404172-G-A
• rs12247672
• ENST00000688440.2:n.369-53293C>T

Variant summary

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

The ENST00000688440.2(HECTD2-AS1):​n.369-53293C>T variant causes a intron 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 ENST00000688440.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750
• Publications: 5 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=-0.84).
• 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 rank	MANE	Protein	UniProt
HECTD2-AS1	NR_024467.1	n.427-53293C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HECTD2-AS1	ENST00000688440.2	n.369-53293C>T		intron_variant	Intron 2 of 3
HECTD2-AS1	ENST00000700888.2	n.219-53293C>T		intron_variant	Intron 3 of 4
HECTD2-AS1	ENST00000838016.1	n.289-53293C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.499 AC: 20707 AN: 41456

American (AMR) AF: 0.0802 AC: 1227 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3470

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5182

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4826

European-Finnish (FIN) AF: 0.0309 AC: 328 AN: 10606

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0476 AC: 3236 AN: 68006

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.0873 Hom.: 6371

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
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs12247672; hg19: chr10-93163929;