rs7635708

Positions:

• chr3-185183233-A-G
• chr3-185183233-A-T

Variant summary

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

The ENST00000417720.1(EHHADH-AS1):​n.1147+293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,108 control chromosomes in the GnomAD database, including 5,374 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 0.21 (5374 hom., cov: 32)
• Consequence: EHHADH-AS1 ENST00000417720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

Genes affected

EHHADH-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EHHADH-AS1	NR_038990.1	n.1147+293A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EHHADH-AS1	ENST00000417720.1	n.1147+293A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32032 AN: 151990 Hom.: 5344 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.211 AC: 32114 AN: 152108 Hom.: 5374 Cov.: 32 AF XY: 0.217 AC XY: 16118 AN XY: 74352

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.191

Alfa AF: 0.124 Hom.: 1133

Bravo AF: 0.227

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.81
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7635708; hg19: chr3-184901021;