chr5-38290100-G-A

Variant names:

• chr5-38290100-G-A
• rs919291
• NM_152403.4:c.97+31249G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001205301.2(EGFLAM):​c.97+31249G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00726 in 152,282 control chromosomes in the GnomAD database, including 18 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 0.0073 (18 hom., cov: 32)
• Consequence: EGFLAM NM_001205301.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

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]

EGFLAM-AS4 (HGNC:41166): (EGFLAM antisense RNA 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00726 (1105/152282) while in subpopulation EAS AF = 0.0456 (236/5170). AF 95% confidence interval is 0.0409. There are 18 homozygotes in GnomAd4. There are 555 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001205301.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGFLAM	NM_152403.4	MANE Select	c.97+31249G>A		intron	N/A	NP_689616.2
	EGFLAM	NM_001205301.2		c.97+31249G>A		intron	N/A	NP_001192230.1
	EGFLAM-AS4	NR_046219.1		n.387+500C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGFLAM	ENST00000322350.10	TSL:1 MANE Select	c.97+31249G>A		intron	N/A	ENSP00000313084.5
	EGFLAM	ENST00000354891.7	TSL:1	c.97+31249G>A		intron	N/A	ENSP00000346964.3
	EGFLAM-AS4	ENST00000512496.1	TSL:1	n.387+500C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00728 AC: 1107 AN: 152164 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.00198

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00648

Gnomad OTH AF: 0.00765

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

GnomAD4 genome AF: 0.00726 AC: 1105 AN: 152282 Hom.: 18 Cov.: 32 AF XY: 0.00745 AC XY: 555 AN XY: 74460

African (AFR) AF: 0.00202 AC: 84 AN: 41562

American (AMR) AF: 0.0102 AC: 156 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.0456 AC: 236 AN: 5170

South Asian (SAS) AF: 0.0339 AC: 163 AN: 4814

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00648 AC: 441 AN: 68022

Other (OTH) AF: 0.00757 AC: 16 AN: 2114

Alfa AF: 0.00678 Hom.: 0

Bravo AF: 0.00746

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.49
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs919291; hg19: chr5-38290202;