rs754146644

Variant names:

• chr17-47341974-G-T
• rs754146644
• NM_152347.5:c.245G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-47341974-G-T
• chr17-47341974-G-A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_152347.5(EFCAB13):​c.245G>T​(p.Gly82Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000484 in 1,445,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: EFCAB13 NM_152347.5 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.330
• Publications: 1 publications found

Genes affected

EFCAB13 (HGNC:26864): (EF-hand calcium binding domain 13)

ENSG00000259753 (HGNC:):

EFCAB13-DT (HGNC:55338): (EFCAB13 divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.038889408).
• BP6: Variant 17-47341974-G-T is Benign according to our data. Variant chr17-47341974-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3506848.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152347.5. 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
	EFCAB13	NM_152347.5	MANE Select	c.245G>T	p.Gly82Val	missense	Exon 6 of 25	NP_689560.3
	EFCAB13	NM_001426585.1		c.245G>T	p.Gly82Val	missense	Exon 5 of 23	NP_001413514.1
	EFCAB13	NM_001426586.1		c.245G>T	p.Gly82Val	missense	Exon 6 of 23	NP_001413515.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB13	ENST00000331493.7	TSL:1 MANE Select	c.245G>T	p.Gly82Val	missense	Exon 6 of 25	ENSP00000332111.2	Q8IY85-1
	ENSG00000259753	ENST00000560629.1	TSL:2	n.*234G>T		non_coding_transcript_exon	Exon 17 of 18	ENSP00000456711.2	H3BM21
	ENSG00000259753	ENST00000560629.1	TSL:2	n.*234G>T		3_prime_UTR	Exon 17 of 18	ENSP00000456711.2	H3BM21

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.0000210 AC: 5 AN: 237582 AF XY: 0.0000155

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000964

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000183

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000484 AC: 7 AN: 1445398 Hom.: 0 Cov.: 28 AF XY: 0.00000278 AC XY: 2 AN XY: 718562

African (AFR) AF: 0.00 AC: 0 AN: 32286

American (AMR) AF: 0.0000713 AC: 3 AN: 42056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25910

East Asian (EAS) AF: 0.00 AC: 0 AN: 38882

South Asian (SAS) AF: 0.00 AC: 0 AN: 82228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53298

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5712

European-Non Finnish (NFE) AF: 0.00000362 AC: 4 AN: 1105250

Other (OTH) AF: 0.00 AC: 0 AN: 59776

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ExAC AF: 0.0000247 AC: 3

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.1
DANN	Benign	0.24
DEOGEN2	Benign	0.0039	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.027	N
LIST_S2	Benign	0.42	T
M_CAP	Benign	0.0046	T
MetaRNN	Benign	0.039	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.46	N
PhyloP100		0.33
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-1.7	N
REVEL	Benign	0.088
Sift	Benign	0.28	T
Sift4G	Benign	0.28	T
Polyphen		0.0010	B
Vest4		0.15
MutPred		0.25		Gain of sheet (P = 0.0101)
MVP		0.014
MPC		0.18
ClinPred		0.029	T
GERP RS		0.30
Varity_R		0.063
gMVP		0.022
Mutation Taster		=95/5	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: rs754146644; hg19: chr17-45419340;