17-30047094-A-G

Variant names:

• chr17-30047094-A-G
• rs7219456
• NM_198529.4:c.1201-4024A>G

Variant summary

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

The NM_198529.4(EFCAB5):​c.1201-4024A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,962 control chromosomes in the GnomAD database, including 20,410 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 0.51 (20410 hom., cov: 32)
• Consequence: EFCAB5 NM_198529.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 8 publications found

Genes affected

EFCAB5 (HGNC:24801): (EF-hand calcium binding domain 5) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198529.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB5	NM_198529.4	MANE Select	c.1201-4024A>G		intron	N/A	NP_940931.3
	EFCAB5	NM_001145053.2		c.1033-4024A>G		intron	N/A	NP_001138525.2
	EFCAB5	NR_026738.2		n.1364-4024A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB5	ENST00000394835.8	TSL:1 MANE Select	c.1201-4024A>G		intron	N/A	ENSP00000378312.3
	EFCAB5	ENST00000588978.1	TSL:1	c.595-4024A>G		intron	N/A	ENSP00000465109.1
	EFCAB5	ENST00000440741.7	TSL:1	n.1201-4024A>G		intron	N/A	ENSP00000393095.2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77902 AN: 151842 Hom.: 20369 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.513 AC: 77995 AN: 151962 Hom.: 20410 Cov.: 32 AF XY: 0.508 AC XY: 37756 AN XY: 74292

African (AFR) AF: 0.571 AC: 23677 AN: 41446

American (AMR) AF: 0.450 AC: 6864 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5164

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4818

European-Finnish (FIN) AF: 0.548 AC: 5791 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34817 AN: 67924

Other (OTH) AF: 0.488 AC: 1028 AN: 2108

Alfa AF: 0.511 Hom.: 3216

Bravo AF: 0.505

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.74
PhyloP100		0.20
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: rs7219456; hg19: chr17-28374112;