14-89903405-C-T

Variant names:

• chr14-89903405-C-T
• rs12889533
• NM_145231.4:c.410+28136G>A

Variant summary

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

The NM_145231.4(EFCAB11):​c.410+28136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,964 control chromosomes in the GnomAD database, including 7,078 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 (7078 hom., cov: 32)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 7 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=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145231.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB11	NM_145231.4	MANE Select	c.410+28136G>A		intron	N/A	NP_660274.1	Q9BUY7-1
	EFCAB11	NM_001284269.2		c.338+28136G>A		intron	N/A	NP_001271198.1	Q9BUY7-2
	EFCAB11	NM_001284267.2		c.266+28136G>A		intron	N/A	NP_001271196.1	Q9BUY7-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB11	ENST00000316738.12	TSL:2 MANE Select	c.410+28136G>A		intron	N/A	ENSP00000326267.7	Q9BUY7-1
	EFCAB11	ENST00000555872.5	TSL:1	c.338+28136G>A		intron	N/A	ENSP00000452320.1	Q9BUY7-2
	EFCAB11	ENST00000905285.1		c.410+28136G>A		intron	N/A	ENSP00000575344.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41769 AN: 151846 Hom.: 7081 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.275 AC: 41750 AN: 151964 Hom.: 7078 Cov.: 32 AF XY: 0.272 AC XY: 20209 AN XY: 74242

African (AFR) AF: 0.0892 AC: 3699 AN: 41460

American (AMR) AF: 0.226 AC: 3454 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3470

East Asian (EAS) AF: 0.148 AC: 765 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4818

European-Finnish (FIN) AF: 0.394 AC: 4135 AN: 10504

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26320 AN: 67950

Other (OTH) AF: 0.284 AC: 599 AN: 2106

Alfa AF: 0.339 Hom.: 15877

Bravo AF: 0.254

Asia WGS AF: 0.194 AC: 673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.58
PhyloP100		0.037
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: rs12889533; hg19: chr14-90369749;