chr17-78315910-T-G

Position:

• chr17-78315910-T-G

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.60+122T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,582 control chromosomes in the GnomAD database, including 5,217 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 0.23 (5203 hom., cov: 32)
  • Exomes 𝑓: 0.21 (14 hom.)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.73+122T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.60+122T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35495 AN: 151910 Hom.: 5201 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.215 AC: 119 AN: 554 Hom.: 14 AF XY: 0.206 AC XY: 73 AN XY: 354

Gnomad4 AFR exome AF: 0.0625

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.583

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.298

Gnomad4 NFE exome AF: 0.184

Gnomad4 OTH exome AF: 0.283

GnomAD4 genome AF: 0.234 AC: 35502 AN: 152028 Hom.: 5203 Cov.: 32 AF XY: 0.242 AC XY: 17962 AN XY: 74310

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.245

Alfa AF: 0.237 Hom.: 7837

Bravo AF: 0.235

Asia WGS AF: 0.495 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4789580; hg19: chr17-76311991;