17-56730348-C-T

Variant names:

• chr17-56730348-C-T
• rs1914986
• ENST00000783597.1:n.178+1070C>T

Variant summary

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

The ENST00000783597.1(ENSG00000302047):​n.178+1070C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,186 control chromosomes in the GnomAD database, including 11,323 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 0.27 (11323 hom., cov: 33)
• Consequence: ENSG00000302047 ENST00000783597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 1 publications found

Genes affected

ENSG00000302047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302047	ENST00000783597.1	n.178+1070C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41379 AN: 152068 Hom.: 11286 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.272 AC: 41465 AN: 152186 Hom.: 11323 Cov.: 33 AF XY: 0.270 AC XY: 20064 AN XY: 74408

African (AFR) AF: 0.709 AC: 29415 AN: 41466

American (AMR) AF: 0.159 AC: 2426 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5182

South Asian (SAS) AF: 0.144 AC: 694 AN: 4828

European-Finnish (FIN) AF: 0.115 AC: 1223 AN: 10604

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5545 AN: 68022

Other (OTH) AF: 0.204 AC: 432 AN: 2116

Alfa AF: 0.190 Hom.: 1042

Bravo AF: 0.297

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.064
DANN	Benign	0.16
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1914986; hg19: chr17-54807709;