17-47316299-T-C

Variant names:

• chr17-47316299-T-C
• rs11650072
• ENST00000560629.1:n.2265+8662T>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+8662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,072 control chromosomes in the GnomAD database, including 28,687 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 0.61 (28687 hom., cov: 33)
• Consequence: ENSG00000259753 ENST00000560629.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 13 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB13-DT	NR_110880.1	n.362+2173A>G		intron_variant	Intron 2 of 2
EFCAB13-DT	NR_110881.1	n.226+2173A>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+8662T>C		intron_variant	Intron 14 of 17	2		ENSP00000456711.2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92580 AN: 151954 Hom.: 28688 Cov.: 33

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.609 AC: 92617 AN: 152072 Hom.: 28687 Cov.: 33 AF XY: 0.608 AC XY: 45214 AN XY: 74344

African (AFR) AF: 0.547 AC: 22672 AN: 41476

American (AMR) AF: 0.515 AC: 7862 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3400 AN: 5184

South Asian (SAS) AF: 0.653 AC: 3153 AN: 4830

European-Finnish (FIN) AF: 0.678 AC: 7156 AN: 10562

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44060 AN: 67968

Other (OTH) AF: 0.618 AC: 1303 AN: 2110

Alfa AF: 0.609 Hom.: 12054

Bravo AF: 0.595

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		0.0020
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: rs11650072; hg19: chr17-45393665;