17-47314438-T-C

Position:

• chr17-47314438-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+4034A>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 0.655 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: EFCAB13-DT NR_110880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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=-0.78).
• 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/exons	MANE	Protein	UniProt
EFCAB13-DT	NR_110880.1	n.362+4034A>G		intron_variant, non_coding_transcript_variant
EFCAB13-DT	NR_110881.1	n.226+4034A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB13-DT	ENST00000575039.1	n.226+4034A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.647

Alfa AF: 0.644 Hom.: 51845

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

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: rs7225700; hg19: chr17-45391804;