rs900382

chr3-129032375-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCC1	NM_001377500.1	c.1139-444C>T		intron_variant		ENST00000683648.1
EFCC1	NM_024768.3	c.1139-447C>T		intron_variant
EFCC1	XM_011513161.3	c.452-444C>T		intron_variant
EFCC1	XM_011513164.3	c.251-444C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCC1	ENST00000683648.1	c.1139-444C>T		intron_variant			NM_001377500.1
EFCC1	ENST00000436022.2	c.1139-447C>T		intron_variant		5		P1
EFCC1	ENST00000481536.2	n.413-447C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0436

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0295

Gnomad4 OTH AF: 0.0559

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.4
Dann	Benign	0.48

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: rs900382; hg19: chr3-128751218;