rs12100561

Variant names:

• chr14-89834691-A-G
• rs12100561
• NM_145231.4:c.411-37367T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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]

ENSG00000259053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EFCAB11	NM_145231.4	c.411-37367T>C		intron_variant	Intron 5 of 5	ENST00000316738.12	NP_660274.1
EFCAB11	NM_001284269.2	c.339-37367T>C		intron_variant	Intron 5 of 5		NP_001271198.1
EFCAB11	NM_001284267.2	c.267-37367T>C		intron_variant	Intron 5 of 5		NP_001271196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB11	ENST00000316738.12	c.411-37367T>C		intron_variant	Intron 5 of 5	2	NM_145231.4	ENSP00000326267.7

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

African (AFR) AF: 0.572 AC: 23710 AN: 41482

American (AMR) AF: 0.773 AC: 11809 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3175 AN: 5160

South Asian (SAS) AF: 0.630 AC: 3040 AN: 4828

European-Finnish (FIN) AF: 0.799 AC: 8459 AN: 10590

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57205 AN: 68010

Other (OTH) AF: 0.758 AC: 1600 AN: 2110

Alfa AF: 0.807 Hom.: 214039

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
PhyloP100		-0.012
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs12100561; hg19: chr14-90301035;