rs12100561

Positions:

• chr14-89834691-A-G
• chr14-89834691-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145231.4(EFCAB11):​c.411-37367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,138 control chromosomes in the GnomAD database, including 42,876 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 0.74 (42876 hom., cov: 33)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

EFCAB11 (HGNC:20357): (EF-hand calcium binding domain 11) Predicted to enable calcium ion binding activity. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB11	NM_145231.4	c.411-37367T>C		intron_variant		ENST00000316738.12
EFCAB11	NM_001284267.2	c.267-37367T>C		intron_variant
EFCAB11	NM_001284269.2	c.339-37367T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB11	ENST00000316738.12	c.411-37367T>C		intron_variant		2	NM_145231.4	P1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112664 AN: 152020 Hom.: 42870 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.741 AC: 112717 AN: 152138 Hom.: 42876 Cov.: 33 AF XY: 0.736 AC XY: 54734 AN XY: 74382

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.758

Alfa AF: 0.822 Hom.: 98668

Bravo AF: 0.735

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs12100561; hg19: chr14-90301035;