rs76795398

Positions:

• chr7-55240511-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000626532.1(ELDR):​n.338-1845T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,242 control chromosomes in the GnomAD database, including 95 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 0.027 (95 hom., cov: 32)
• Consequence: ELDR ENST00000626532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

ELDR (HGNC:49511): (EGFR long non-coding downstream RNA) Predicted to act upstream of or within regulation of gene expression and response to wounding. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.027 (4114/152242) while in subpopulation NFE AF= 0.0424 (2883/68016). AF 95% confidence interval is 0.0411. There are 95 homozygotes in gnomad4. There are 1941 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELDR	NR_110426.1	n.338-1845T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELDR	ENST00000626532.1	n.338-1845T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4117 AN: 152124 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.00637

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0270 AC: 4114 AN: 152242 Hom.: 95 Cov.: 32 AF XY: 0.0261 AC XY: 1941 AN XY: 74428

Gnomad4 AFR AF: 0.00636

Gnomad4 AMR AF: 0.0234

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0424

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0369 Hom.: 28

Bravo AF: 0.0264

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76795398; hg19: chr7-55308204;