5-38440499-A-T

Variant names:

• chr5-38440499-A-T
• NM_152403.4:c.2464+2044A>T

Variant summary

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

The NM_152403.4(EGFLAM):​c.2464+2044A>T 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: 32)
• Consequence: EGFLAM NM_152403.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

EGFLAM (HGNC:26810): (EGF like, fibronectin type III and laminin G domains) Predicted to enable calcium ion binding activity and glycosaminoglycan binding activity. Predicted to be involved in animal organ morphogenesis and tissue development. Predicted to act upstream of or within extracellular matrix organization; peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan; and positive regulation of cell-substrate adhesion. Part of cell surface. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGFLAM	NM_152403.4	c.2464+2044A>T		intron_variant	Intron 17 of 21	ENST00000322350.10	NP_689616.2
EGFLAM	NM_001205301.2	c.2464+2044A>T		intron_variant	Intron 17 of 22		NP_001192230.1
EGFLAM	NM_182798.3	c.1762+2044A>T		intron_variant	Intron 12 of 16		NP_877950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGFLAM	ENST00000322350.10	c.2464+2044A>T		intron_variant	Intron 17 of 21	1	NM_152403.4	ENSP00000313084.5
EGFLAM	ENST00000354891.7	c.2464+2044A>T		intron_variant	Intron 17 of 22	1		ENSP00000346964.3
EGFLAM	ENST00000397202.6	c.562+2044A>T		intron_variant	Intron 7 of 11	1		ENSP00000380385.2
EGFLAM	ENST00000336740.10	c.1762+2044A>T		intron_variant	Intron 12 of 16	2		ENSP00000337607.6

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.67

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: chr5-38440601;