chr14-89818395-A-G

Variant names:

• chr14-89818395-A-G
• rs8013403
• NM_145231.4:c.411-21071T>C

Variant summary

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

The NM_145231.4(EFCAB11):​c.411-21071T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,756 control chromosomes in the GnomAD database, including 6,282 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 0.27 (6282 hom., cov: 31)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 2 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB11	NM_145231.4	c.411-21071T>C		intron_variant	Intron 5 of 5	ENST00000316738.12	NP_660274.1
EFCAB11	NM_001284269.2	c.339-21071T>C		intron_variant	Intron 5 of 5		NP_001271198.1
EFCAB11	NM_001284267.2	c.267-21071T>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.411-21071T>C		intron_variant	Intron 5 of 5	2	NM_145231.4	ENSP00000326267.7

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40691 AN: 151638 Hom.: 6284 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.268 AC: 40716 AN: 151756 Hom.: 6282 Cov.: 31 AF XY: 0.270 AC XY: 20025 AN XY: 74156

African (AFR) AF: 0.373 AC: 15416 AN: 41304

American (AMR) AF: 0.290 AC: 4424 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3466

East Asian (EAS) AF: 0.570 AC: 2921 AN: 5126

South Asian (SAS) AF: 0.294 AC: 1409 AN: 4794

European-Finnish (FIN) AF: 0.175 AC: 1844 AN: 10562

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12883 AN: 67930

Other (OTH) AF: 0.269 AC: 566 AN: 2108

Alfa AF: 0.229 Hom.: 12981

Bravo AF: 0.287

Asia WGS AF: 0.400 AC: 1396 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.87
PhyloP100		0.22
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)		0.040		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: rs8013403; hg19: chr14-90284739;