rs11868369

Positions:

• chr17-70319165-G-A

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, non coding transcript 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: ENST00000592809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000592809.1	n.177-5777C>T		intron_variant, non_coding_transcript_variant		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;