rs2819358

Variant names:

• chr1-202007274-T-G
• rs2819358
• ENST00000419190.2:n.664+2526A>C

Variant summary

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

The ENST00000419190.2(ELF3-AS1):​n.664+2526A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,106 control chromosomes in the GnomAD database, including 32,435 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 0.64 (32435 hom., cov: 33)
• Consequence: ELF3-AS1 ENST00000419190.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 1 publications found

Genes affected

ELF3-AS1 (HGNC:40211): (ELF3 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 (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF3-AS1	NR_146472.1	n.554+2526A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELF3-AS1	ENST00000419190.2	n.664+2526A>C		intron_variant	Intron 1 of 1	2
ELF3-AS1	ENST00000719677.1	n.226+834A>C		intron_variant	Intron 1 of 1
ELF3-AS1	ENST00000719678.1	n.172+834A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97321 AN: 151988 Hom.: 32370 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.641 AC: 97454 AN: 152106 Hom.: 32435 Cov.: 33 AF XY: 0.644 AC XY: 47901 AN XY: 74346

African (AFR) AF: 0.822 AC: 34142 AN: 41518

American (AMR) AF: 0.554 AC: 8467 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1892 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2974 AN: 5156

South Asian (SAS) AF: 0.776 AC: 3748 AN: 4830

European-Finnish (FIN) AF: 0.614 AC: 6486 AN: 10562

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37775 AN: 67960

Other (OTH) AF: 0.601 AC: 1270 AN: 2114

Alfa AF: 0.589 Hom.: 19032

Bravo AF: 0.639

Asia WGS AF: 0.744 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2819358; hg19: chr1-201976402;