ENST00000563715.2:n.420-1896T>C

Variant names:

• chr22-43815018-T-C
• rs5764318
• ENST00000563715.2:n.420-1896T>C

Variant summary

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

The ENST00000563715.2(EFCAB6-DT):​n.420-1896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,226 control chromosomes in the GnomAD database, including 1,531 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 0.13 (1531 hom., cov: 32)
• Consequence: EFCAB6-DT ENST00000563715.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 8 publications found

Genes affected

EFCAB6-DT (HGNC:55371): (EFCAB6 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB6-DT	NR_186820.1	n.413-1896T>C		intron_variant	Intron 1 of 1
EFCAB6-DT	NR_186821.1	n.413-533T>C		intron_variant	Intron 1 of 1
EFCAB6-DT	NR_186822.1	n.564-1896T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB6-DT	ENST00000563715.2	n.420-1896T>C		intron_variant	Intron 1 of 1	3
EFCAB6-DT	ENST00000763788.1	n.65-1896T>C		intron_variant	Intron 1 of 1
EFCAB6-DT	ENST00000763789.1	n.474+1231T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20018 AN: 152108 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.132 AC: 20030 AN: 152226 Hom.: 1531 Cov.: 32 AF XY: 0.132 AC XY: 9830 AN XY: 74414

African (AFR) AF: 0.0386 AC: 1606 AN: 41556

American (AMR) AF: 0.119 AC: 1826 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3472

East Asian (EAS) AF: 0.178 AC: 920 AN: 5170

South Asian (SAS) AF: 0.200 AC: 967 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10588

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11841 AN: 68004

Other (OTH) AF: 0.159 AC: 336 AN: 2114

Alfa AF: 0.162 Hom.: 3595

Bravo AF: 0.121

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.5
DANN	Benign	0.88
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs5764318; hg19: chr22-44210898;