rs7219456

chr17-30047094-A-Gchr17-30047094-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB5	NM_198529.4	c.1201-4024A>G		intron_variant		ENST00000394835.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB5	ENST00000394835.8	c.1201-4024A>G		intron_variant		1	NM_198529.4	P1

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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.488

Alfa AF: 0.510 Hom.: 3100

Bravo AF: 0.505

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.9
Dann	Benign	0.74

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: rs7219456; hg19: chr17-28374112;