chr3-129032375-C-T

Variant names:

• chr3-129032375-C-T
• rs900382
• NM_001377500.1:c.1139-444C>T

Variant summary

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

The NM_001377500.1(EFCC1):​c.1139-444C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 151,906 control chromosomes in the GnomAD database, including 732 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 0.064 (732 hom., cov: 32)
• Consequence: EFCC1 NM_001377500.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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.1139-444C>T		intron	N/A	NP_001364429.1
	EFCC1	NM_024768.3		c.1139-447C>T		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.1139-444C>T		intron	N/A	ENSP00000507795.1
	ENSG00000303956	ENST00000798368.1		n.226G>A		non_coding_transcript_exon	Exon 2 of 3
	EFCC1	ENST00000436022.2	TSL:5	c.1139-447C>T		intron	N/A	ENSP00000414597.3

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9729 AN: 151788 Hom.: 735 Cov.: 32

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0641 AC: 9732 AN: 151906 Hom.: 732 Cov.: 32 AF XY: 0.0690 AC XY: 5120 AN XY: 74256

African (AFR) AF: 0.0583 AC: 2412 AN: 41396

American (AMR) AF: 0.110 AC: 1683 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3466

East Asian (EAS) AF: 0.393 AC: 2018 AN: 5134

South Asian (SAS) AF: 0.160 AC: 767 AN: 4798

European-Finnish (FIN) AF: 0.0526 AC: 556 AN: 10574

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0295 AC: 2002 AN: 67954

Other (OTH) AF: 0.0559 AC: 118 AN: 2112

Alfa AF: 0.0458 Hom.: 43

Bravo AF: 0.0696

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		0.29
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: rs900382; hg19: chr3-128751218;