chr10-91600573-C-T

Variant names:

• chr10-91600573-C-T
• rs11597974
• ENST00000838016.1:n.166+13053G>A

Variant summary

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

The ENST00000838016.1(HECTD2-AS1):​n.166+13053G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,158 control chromosomes in the GnomAD database, including 1,253 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 0.12 (1253 hom., cov: 32)
• Consequence: HECTD2-AS1 ENST00000838016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HECTD2-AS1	NR_024467.1		n.110+10778G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HECTD2-AS1	ENST00000838016.1		n.166+13053G>A		intron	N/A
	HECTD2-AS1	ENST00000838017.1		n.250+10684G>A		intron	N/A
	HECTD2-AS1	ENST00000838018.1		n.127+10778G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18269 AN: 152040 Hom.: 1252 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.120 AC: 18298 AN: 152158 Hom.: 1253 Cov.: 32 AF XY: 0.120 AC XY: 8931 AN XY: 74394

African (AFR) AF: 0.188 AC: 7817 AN: 41498

American (AMR) AF: 0.137 AC: 2098 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.109 AC: 559 AN: 5150

South Asian (SAS) AF: 0.116 AC: 558 AN: 4824

European-Finnish (FIN) AF: 0.0898 AC: 953 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5813 AN: 67988

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.0881 Hom.: 808

Bravo AF: 0.127

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.65
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs11597974; hg19: chr10-93360330;