chr3-185181469-A-G

Variant names:

• chr3-185181469-A-G
• rs6784193
• ENST00000417720.1:n.821A>G

Variant summary

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

The ENST00000417720.1(EHHADH-AS1):​n.821A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,276 control chromosomes in the GnomAD database, including 9,926 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 0.31 (9924 hom., cov: 32)
  • Exomes 𝑓: 0.16 (2 hom.)
• Consequence: EHHADH-AS1 ENST00000417720.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EHHADH-AS1	NR_038990.1	n.821A>G		non_coding_transcript_exon_variant	Exon 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EHHADH-AS1	ENST00000417720.1	n.821A>G		non_coding_transcript_exon_variant	Exon 5 of 7	1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46973 AN: 152024 Hom.: 9876 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.270

GnomAD4 exome AF: 0.164 AC: 22 AN: 134 Hom.: 2 Cov.: 0 AF XY: 0.152 AC XY: 10 AN XY: 66

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.164 AC: 21 AN: 128

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.309 AC: 47080 AN: 152142 Hom.: 9924 Cov.: 32 AF XY: 0.314 AC XY: 23384 AN XY: 74366

African (AFR) AF: 0.552 AC: 22891 AN: 41492

American (AMR) AF: 0.334 AC: 5109 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3550 AN: 5174

South Asian (SAS) AF: 0.344 AC: 1661 AN: 4822

European-Finnish (FIN) AF: 0.166 AC: 1755 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10960 AN: 68014

Other (OTH) AF: 0.271 AC: 571 AN: 2108

Alfa AF: 0.205 Hom.: 4137

Bravo AF: 0.331

Asia WGS AF: 0.484 AC: 1682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.73
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs6784193; hg19: chr3-184899257;