rs1721492

Variant names:

• chr7-105585733-T-C
• rs1721492
• ENST00000469099.5:c.-81+5572A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000295921 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB10	ENST00000469099.5	c.-81+5572A>G		intron_variant	Intron 1 of 3	3		ENSP00000495682.1
EFCAB10	ENST00000490493.1	c.-81+5572A>G		intron_variant	Intron 2 of 4	3		ENSP00000494437.1
ENSG00000295921	ENST00000733939.1	n.108+2802T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.446 AC: 18446 AN: 41390

American (AMR) AF: 0.260 AC: 3970 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1156 AN: 5176

South Asian (SAS) AF: 0.309 AC: 1486 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3154 AN: 10568

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16032 AN: 67958

Other (OTH) AF: 0.288 AC: 608 AN: 2110

Alfa AF: 0.254 Hom.: 19746

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1721492; hg19: chr7-105226180;