rs6783938

Variant names:

• chr3-185188413-C-T
• rs6783938
• ENST00000417720.1:n.1148-3274C>T

Variant summary

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

The ENST00000417720.1(EHHADH-AS1):​n.1148-3274C>T variant causes a intron 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 ENST00000417720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EHHADH-AS1	NR_038990.1	n.1148-3274C>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EHHADH-AS1	ENST00000417720.1	n.1148-3274C>T		intron_variant	Intron 6 of 6	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

African (AFR) AF: 0.460 AC: 19076 AN: 41450

American (AMR) AF: 0.184 AC: 2810 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0773 AC: 268 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5178

South Asian (SAS) AF: 0.183 AC: 881 AN: 4812

European-Finnish (FIN) AF: 0.100 AC: 1063 AN: 10594

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7054 AN: 68002

Other (OTH) AF: 0.163 AC: 344 AN: 2114

Alfa AF: 0.141 Hom.: 2886

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs6783938; hg19: chr3-184906201;