17-47316299-T-C

Variant summary

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

The NR_110880.1(EFCAB13-DT):n.362+2173A>G variant causes a intron, non coding transcript 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: EFCAB13-DT NR_110880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
EFCAB13-DT	NR_110880.1	n.362+2173A>G		intron_variant, non_coding_transcript_variant
EFCAB13-DT	NR_110881.1	n.226+2173A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB13-DT	ENST00000575039.1	n.226+2173A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.618

Alfa AF: 0.608 Hom.: 9676

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11650072; hg19: chr17-45393665;