rs11868369

Variant names:

• chr17-70319165-G-A
• rs11868369
• ENST00000592809.1:n.177-5777C>T

Variant summary

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

The ENST00000592809.1(ENSG00000267109):​n.177-5777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,102 control chromosomes in the GnomAD database, including 3,268 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 0.20 (3268 hom., cov: 32)
• Consequence: ENSG00000267109 ENST00000592809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

ENSG00000267109 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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
ENSG00000267109	ENST00000592809.1	n.177-5777C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30590 AN: 151984 Hom.: 3267 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.201 AC: 30609 AN: 152102 Hom.: 3268 Cov.: 32 AF XY: 0.200 AC XY: 14834 AN XY: 74346

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.190

Alfa AF: 0.216 Hom.: 892

Bravo AF: 0.193

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11868369; hg19: chr17-68315306;