rs6783938

chr3-185188413-C-T

Variant summary

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

The NR_038990.1(EHHADH-AS1):n.1148-3274C>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 0.215 in 152,110 control chromosomes in the GnomAD database, including 5,383 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 0.22 (5383 hom., cov: 32)
• Consequence: EHHADH-AS1 NR_038990.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781

Genes affected

EHHADH-AS1 (HGNC:44133): (EHHADH antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHHADH-AS1	NR_038990.1	n.1148-3274C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHHADH-AS1	ENST00000417720.1	n.1148-3274C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32669 AN: 151992 Hom.: 5344 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.215 AC: 32765 AN: 152110 Hom.: 5383 Cov.: 32 AF XY: 0.217 AC XY: 16125 AN XY: 74366

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0773

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.163

Alfa AF: 0.127 Hom.: 1713

Bravo AF: 0.230

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.13
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6783938; hg19: chr3-184906201;