14-89903405-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB11	NM_145231.4	c.410+28136G>A		intron_variant	Intron 5 of 5	ENST00000316738.12	NP_660274.1
EFCAB11	NM_001284269.2	c.338+28136G>A		intron_variant	Intron 5 of 5		NP_001271198.1
EFCAB11	NM_001284267.2	c.266+28136G>A		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.410+28136G>A		intron_variant	Intron 5 of 5	2	NM_145231.4	ENSP00000326267.7

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

Gnomad4 AFR AF: 0.0892

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.284

Alfa AF: 0.347 Hom.: 12936

Bravo AF: 0.254

Asia WGS AF: 0.194 AC: 673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.58

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: rs12889533; hg19: chr14-90369749;