NM_172373.4:c.173A>T

Variant names:

• chr13-40958916-T-A
• NM_172373.4:c.173A>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_172373.4(ELF1):​c.173A>T​(p.Asn58Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,730 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N58S) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: ELF1 NM_172373.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

Genes affected

ELF1 (HGNC:3316): (E74 like ETS transcription factor 1) This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF1	NM_172373.4	c.173A>T	p.Asn58Ile	missense_variant	Exon 3 of 9	ENST00000239882.7	NP_758961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELF1	ENST00000239882.7	c.173A>T	p.Asn58Ile	missense_variant	Exon 3 of 9	1	NM_172373.4	ENSP00000239882.3
ELF1	ENST00000635415.1	c.173A>T	p.Asn58Ile	missense_variant	Exon 3 of 9	5		ENSP00000489586.1
ELF1	ENST00000625359.1	c.173A>T	p.Asn58Ile	missense_variant	Exon 2 of 8	2		ENSP00000486912.1
ELF1	ENST00000498824.4	n.173A>T		non_coding_transcript_exon_variant	Exon 2 of 9	2		ENSP00000487240.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461730 Hom.: 0 Cov.: 56 AF XY: 0.00000138 AC XY: 1 AN XY: 727182

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.078	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.47	T;.;T
Eigen	Benign	0.18
Eigen_PC	Benign	0.13
FATHMM_MKL	Benign	0.66	D
LIST_S2	Uncertain	0.90	D;D;D
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.46	T;T;T
MetaSVM	Benign	-0.63	T
MutationAssessor	Uncertain	2.2	M;M;.
PrimateAI	Benign	0.45	T
PROVEAN	Pathogenic	-5.0	D;.;.
REVEL	Benign	0.14
Sift	Uncertain	0.0010	D;.;.
Sift4G	Uncertain	0.0040	D;D;.
Polyphen		0.95	P;.;.
Vest4		0.46
MutPred		0.43		Loss of sheet (P = 0.0126);Loss of sheet (P = 0.0126);Loss of sheet (P = 0.0126);
MVP		0.35
MPC		0.59
ClinPred		0.99	D
GERP RS		0.35
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.48
gMVP		0.50

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: chr13-41533052;