17-78347880-T-C

Variant names:

• chr17-78347880-T-C
• rs11077359
• ENST00000794841.1:n.139-2277A>G

Variant summary

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

The ENST00000794841.1(ENSG00000303469):​n.139-2277A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,180 control chromosomes in the GnomAD database, including 43,693 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 0.75 (43672 hom., cov: 31)
  • Exomes 𝑓: 0.80 (21 hom.)
• Consequence: ENSG00000303469 ENST00000794841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 3 publications found

Genes affected

ENSG00000303469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 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
ENSG00000303469	ENST00000794841.1	n.139-2277A>G		intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794842.1	n.136-2277A>G		intron_variant	Intron 1 of 1
ENSG00000303469	ENST00000794843.1	n.213-2277A>G		intron_variant	Intron 2 of 2
ENSG00000267737	ENST00000586321.1	n.*82T>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114313 AN: 152002 Hom.: 43649 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.760

GnomAD4 exome AF: 0.800 AC: 48 AN: 60 Hom.: 21 AF XY: 0.875 AC XY: 42 AN XY: 48

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.667 AC: 4 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.795 AC: 35 AN: 44

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.752 AC: 114382 AN: 152120 Hom.: 43672 Cov.: 31 AF XY: 0.757 AC XY: 56300 AN XY: 74362

African (AFR) AF: 0.610 AC: 25297 AN: 41468

American (AMR) AF: 0.806 AC: 12325 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2851 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4842 AN: 5160

South Asian (SAS) AF: 0.806 AC: 3893 AN: 4830

European-Finnish (FIN) AF: 0.841 AC: 8907 AN: 10594

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53613 AN: 67984

Other (OTH) AF: 0.761 AC: 1608 AN: 2112

Alfa AF: 0.773 Hom.: 78724

Bravo AF: 0.745

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.8
DANN	Benign	0.60
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs11077359; hg19: chr17-76343961;