chr7-1706496-T-C

Position:

• chr7-1706496-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELFN1	NM_001128636.4	c.-455-2595T>C		intron_variant		ENST00000424383.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELFN1	ENST00000424383.5	c.-455-2595T>C		intron_variant		5	NM_001128636.4	P1
ELFN1	ENST00000561626.4	c.-452-2595T>C		intron_variant		2		P1
ELFN1	ENST00000691883.1	c.-455-2595T>C		intron_variant				P1
ELFN1	ENST00000688716.1	n.191-2595T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.281

Alfa AF: 0.225 Hom.: 2157

Bravo AF: 0.314

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.40

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: rs7783310; hg19: chr7-1746132;