1-63576116-C-T

Position:

• chr1-63576116-C-T

Variant summary

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

The XM_011542301.3(EFCAB7):​c.1854+4988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,996 control chromosomes in the GnomAD database, including 29,473 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 0.60 (29473 hom., cov: 31)
• Consequence: EFCAB7 XM_011542301.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

Genes affected

EFCAB7 (HGNC:29379): (EF-hand calcium binding domain 7) Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of protein import into nucleus; positive regulation of protein localization to ciliary membrane; and positive regulation of transcription by RNA polymerase II. Predicted to be located in ciliary membrane. Predicted to be extrinsic component of membrane. Predicted to be part of plasma membrane protein complex. [provided by Alliance of Genome Resources, Apr 2022]

ITGB3BP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB7	XM_011542301.3	c.1854+4988C>T		intron_variant			XP_011540603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB3BP	ENST00000478138.1	n.197+17409G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91699 AN: 151876 Hom.: 29426 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.604 AC: 91798 AN: 151996 Hom.: 29473 Cov.: 31 AF XY: 0.602 AC XY: 44763 AN XY: 74300

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.607

Alfa AF: 0.527 Hom.: 9911

Bravo AF: 0.630

Asia WGS AF: 0.656 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs217463; hg19: chr1-64041787;