7-1706496-T-C

Variant names:

• chr7-1706496-T-C
• rs7783310
• NM_001128636.4:c.-455-2595T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128636.4(ELFN1):​c.-455-2595T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,966 control chromosomes in the GnomAD database, including 9,272 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 0.30 (9272 hom., cov: 33)
• Consequence: ELFN1 NM_001128636.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 publications found

Genes affected

ELFN1 (HGNC:33154): (extracellular leucine rich repeat and fibronectin type III domain containing 1) Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synapse organization. Predicted to be located in dendrite and excitatory synapse. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128636.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELFN1	NM_001128636.4	MANE Select	c.-455-2595T>C		intron	N/A	NP_001122108.1
	ELFN1	NM_001394187.1		c.-455-2595T>C		intron	N/A	NP_001381116.1
	ELFN1	NM_001394188.1		c.-455-2595T>C		intron	N/A	NP_001381117.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELFN1	ENST00000424383.5	TSL:5 MANE Select	c.-455-2595T>C		intron	N/A	ENSP00000456548.1
	ELFN1	ENST00000561626.4	TSL:2	c.-452-2595T>C		intron	N/A	ENSP00000457193.1
	ELFN1	ENST00000691883.1		c.-455-2595T>C		intron	N/A	ENSP00000510296.1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45980 AN: 151850 Hom.: 9251 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.303 AC: 46049 AN: 151966 Hom.: 9272 Cov.: 33 AF XY: 0.301 AC XY: 22347 AN XY: 74296

African (AFR) AF: 0.567 AC: 23492 AN: 41424

American (AMR) AF: 0.176 AC: 2692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2531 AN: 5154

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4816

European-Finnish (FIN) AF: 0.167 AC: 1772 AN: 10582

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12626 AN: 67926

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.231 Hom.: 2561

Bravo AF: 0.314

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs7783310; hg19: chr7-1746132;