3-129032259-G-C

Variant names:

• chr3-129032259-G-C
• rs2341295
• NM_001377500.1:c.1139-560G>C

Variant summary

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

The NM_001377500.1(EFCC1):​c.1139-560G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,132 control chromosomes in the GnomAD database, including 9,805 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 0.34 (9805 hom., cov: 33)
• Consequence: EFCC1 NM_001377500.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 3 publications found

Genes affected

EFCC1 (HGNC:25692): (EF-hand and coiled-coil domain containing 1) Predicted to enable calcium ion binding activity. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377500.1. 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
	EFCC1	NM_001377500.1	MANE Select	c.1139-560G>C		intron	N/A	NP_001364429.1
	EFCC1	NM_024768.3		c.1139-563G>C		intron	N/A	NP_079044.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCC1	ENST00000683648.1	MANE Select	c.1139-560G>C		intron	N/A	ENSP00000507795.1
	EFCC1	ENST00000436022.2	TSL:5	c.1139-563G>C		intron	N/A	ENSP00000414597.3
	EFCC1	ENST00000481536.2	TSL:2	n.413-563G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52454 AN: 152014 Hom.: 9808 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.345 AC: 52449 AN: 152132 Hom.: 9805 Cov.: 33 AF XY: 0.341 AC XY: 25386 AN XY: 74374

African (AFR) AF: 0.219 AC: 9090 AN: 41470

American (AMR) AF: 0.290 AC: 4435 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1171 AN: 5180

South Asian (SAS) AF: 0.339 AC: 1637 AN: 4830

European-Finnish (FIN) AF: 0.427 AC: 4520 AN: 10586

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28833 AN: 67996

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.263 Hom.: 691

Bravo AF: 0.329

Asia WGS AF: 0.260 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.49
PhyloP100		-0.0070
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: rs2341295; hg19: chr3-128751102;