rs1721492

chr7-105585733-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000469099.5(EFCAB10):c.-81+5572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,958 control chromosomes in the GnomAD database, including 7,610 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 0.30 (7610 hom., cov: 32)
• Consequence: EFCAB10 ENST00000469099.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

EFCAB10 (HGNC:34531): (EF-hand calcium binding domain 10) 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB10	ENST00000469099.5	c.-81+5572A>G		intron_variant		3
EFCAB10	ENST00000490493.1	c.-81+5572A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45762 AN: 151840 Hom.: 7598 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.301 AC: 45803 AN: 151958 Hom.: 7610 Cov.: 32 AF XY: 0.304 AC XY: 22574 AN XY: 74276

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.288

Alfa AF: 0.246 Hom.: 7849

Bravo AF: 0.306

Asia WGS AF: 0.257 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.38
Dann	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1721492; hg19: chr7-105226180;