chrX-44325676-A-T

Variant names:

• chrX-44325676-A-T
• rs1562875
• NM_025184.4:c.43-12920T>A

Variant summary

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

The NM_025184.4(EFHC2):​c.43-12920T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.074 (440 hom., 2236 hem., cov: 20)
• Consequence: EFHC2 NM_025184.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 1 publications found

Genes affected

EFHC2 (HGNC:26233): (EF-hand domain containing 2) This gene encodes a protein which contains three DM10 domains and three calcium-binding EF-hand motifs. A related protein is encoded by a gene on chromosome 6. It has been suggested that both proteins are involved in the development of epilepsy (PMID: 15258581, 16112844) and that this gene may be associated with fear recognition in individuals with Turner syndrome. [provided by RefSeq, Aug 2011]

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 (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFHC2	NM_025184.4	c.43-12920T>A		intron_variant	Intron 1 of 14	ENST00000420999.2	NP_079460.2
EFHC2	XM_047442535.1	c.43-12920T>A		intron_variant	Intron 1 of 13		XP_047298491.1
EFHC2	XM_047442536.1	c.43-12920T>A		intron_variant	Intron 1 of 14		XP_047298492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFHC2	ENST00000420999.2	c.43-12920T>A		intron_variant	Intron 1 of 14	1	NM_025184.4	ENSP00000404232.2

Frequencies

GnomAD3 genomes AF: 0.0737 AC: 7889 AN: 106976 Hom.: 438 Cov.: 20

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0936

Gnomad MID AF: 0.0812

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0737 AC: 7893 AN: 107033 Hom.: 440 Cov.: 20 AF XY: 0.0759 AC XY: 2236 AN XY: 29479

African (AFR) AF: 0.0127 AC: 376 AN: 29550

American (AMR) AF: 0.157 AC: 1486 AN: 9482

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 338 AN: 2582

East Asian (EAS) AF: 0.409 AC: 1361 AN: 3328

South Asian (SAS) AF: 0.135 AC: 315 AN: 2328

European-Finnish (FIN) AF: 0.0936 AC: 489 AN: 5223

Middle Eastern (MID) AF: 0.0888 AC: 19 AN: 214

European-Non Finnish (NFE) AF: 0.0637 AC: 3324 AN: 52216

Other (OTH) AF: 0.0804 AC: 116 AN: 1443

Alfa AF: 0.0710 Hom.: 389

Bravo AF: 0.0856

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.41
PhyloP100		-0.28
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: rs1562875; hg19: chrX-44184922;