17-47314438-T-C

Variant names:

• chr17-47314438-T-C
• rs7225700
• ENST00000560629.1:n.2265+6801T>C

Variant summary

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

The ENST00000560629.1(ENSG00000259753):​n.2265+6801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,292 control chromosomes in the GnomAD database, including 32,741 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 0.65 (32741 hom., cov: 30)
• Consequence: ENSG00000259753 ENST00000560629.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 27 publications found

Genes affected

ENSG00000259753 (HGNC:):

EFCAB13-DT (HGNC:55338): (EFCAB13 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB13-DT	NR_110880.1	n.362+4034A>G		intron_variant	Intron 2 of 2
EFCAB13-DT	NR_110881.1	n.226+4034A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259753	ENST00000560629.1	n.2265+6801T>C		intron_variant	Intron 14 of 17	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes AF: 0.655 AC: 98998 AN: 151174 Hom.: 32734 Cov.: 30

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.655 AC: 99054 AN: 151292 Hom.: 32741 Cov.: 30 AF XY: 0.652 AC XY: 48159 AN XY: 73882

African (AFR) AF: 0.703 AC: 28983 AN: 41230

American (AMR) AF: 0.536 AC: 8105 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2192 AN: 3464

East Asian (EAS) AF: 0.661 AC: 3395 AN: 5138

South Asian (SAS) AF: 0.645 AC: 3084 AN: 4784

European-Finnish (FIN) AF: 0.678 AC: 7053 AN: 10406

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44060 AN: 67856

Other (OTH) AF: 0.647 AC: 1360 AN: 2102

Alfa AF: 0.647 Hom.: 85631

Bravo AF: 0.647

Asia WGS AF: 0.640 AC: 2224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.7
DANN	Benign	0.77
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7225700; hg19: chr17-45391804;