17-78338705-G-C

Position:

• chr17-78338705-G-C

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-5260G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,142 control chromosomes in the GnomAD database, including 29,093 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 (29093 hom., cov: 28)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.74-5260G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.61-5260G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91404 AN: 151024 Hom.: 29085 Cov.: 28

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.605 AC: 91460 AN: 151142 Hom.: 29093 Cov.: 28 AF XY: 0.608 AC XY: 44821 AN XY: 73726

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.614

Alfa AF: 0.629 Hom.: 3873

Bravo AF: 0.591

Asia WGS AF: 0.704 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501199; hg19: chr17-76334786;