3-129032259-G-C

Position:

• chr3-129032259-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCC1	NM_001377500.1	c.1139-560G>C		intron_variant		ENST00000683648.1
EFCC1	NM_024768.3	c.1139-563G>C		intron_variant
EFCC1	XM_011513161.3	c.452-560G>C		intron_variant
EFCC1	XM_011513164.3	c.251-560G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCC1	ENST00000683648.1	c.1139-560G>C		intron_variant			NM_001377500.1
EFCC1	ENST00000436022.2	c.1139-563G>C		intron_variant		5		P1
EFCC1	ENST00000481536.2	n.413-563G>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.368

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.49

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: rs2341295; hg19: chr3-128751102;