rs11868369

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000267109 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592809.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267109	ENST00000592809.1	TSL:3	n.177-5777C>T		intron	N/A

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

African (AFR) AF: 0.203 AC: 8423 AN: 41490

American (AMR) AF: 0.153 AC: 2336 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3466

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5174

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4818

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14974 AN: 67972

Other (OTH) AF: 0.190 AC: 402 AN: 2114

Alfa AF: 0.207 Hom.: 1606

Bravo AF: 0.193

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.25
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11868369; hg19: chr17-68315306;