19-48024325-C-T

Variant names:

• chr19-48024325-C-T
• rs3936340
• NM_022142.5:c.*8-627C>T

Variant summary

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

The NM_022142.5(ELSPBP1):​c.*8-627C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,146 control chromosomes in the GnomAD database, including 64,656 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 0.92 (64656 hom., 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELSPBP1	NM_022142.5	c.*8-627C>T		intron_variant	Intron 6 of 6	ENST00000339841.7	NP_071425.3
ELSPBP1	XM_017027130.2	c.*8-627C>T		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>T		intron_variant	Intron 6 of 6	1	NM_022142.5	ENSP00000340660.2
ELSPBP1	ENST00000593782.1	c.*50-627C>T		intron_variant	Intron 3 of 3	5		ENSP00000472960.1
ELSPBP1	ENST00000593413.1	c.*8-606C>T		intron_variant	Intron 2 of 2	3		ENSP00000470551.1
ELSPBP1	ENST00000597519.5	c.*8-627C>T		intron_variant	Intron 3 of 3	3		ENSP00000471690.1

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140111 AN: 152028 Hom.: 64611 Cov.: 30

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.922 AC: 140214 AN: 152146 Hom.: 64656 Cov.: 30 AF XY: 0.920 AC XY: 68420 AN XY: 74376

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.921

Alfa AF: 0.914 Hom.: 143739

Bravo AF: 0.921

Asia WGS AF: 0.870 AC: 3025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.30

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

LitVar

Other links and lift over

dbSNP: rs3936340; hg19: chr19-48527582;