19-48024325-C-G

Variant names:

• chr19-48024325-C-G
• NM_022142.5:c.*8-627C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022142.5(ELSPBP1):​c.*8-627C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: ELSPBP1 NM_022142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

ELSPBP1 (HGNC:14417): (epididymal sperm binding protein 1) The protein encoded by this gene belongs to the sperm-coating protein family of epididymal origin. This protein and its canine homolog are the first known examples of proteins with four tandemly arranged fibronectin type 2 (Fn2) domains in the Fn2-module protein family. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELSPBP1	NM_022142.5	c.*8-627C>G		intron_variant	Intron 6 of 6	ENST00000339841.7	NP_071425.3
ELSPBP1	XM_017027130.2	c.*8-627C>G		intron_variant	Intron 6 of 6		XP_016882619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELSPBP1	ENST00000339841.7	c.*8-627C>G		intron_variant	Intron 6 of 6	1	NM_022142.5	ENSP00000340660.2
ELSPBP1	ENST00000593782.1	c.*50-627C>G		intron_variant	Intron 3 of 3	5		ENSP00000472960.1
ELSPBP1	ENST00000593413.1	c.*8-606C>G		intron_variant	Intron 2 of 2	3		ENSP00000470551.1
ELSPBP1	ENST00000597519.5	c.*8-627C>G		intron_variant	Intron 3 of 3	3		ENSP00000471690.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-48527582;