rs17069951

Variant names:

• chr6-140395916-C-T
• rs17069951
• ENST00000684511.1:n.35+80982C>T

Variant summary

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

The ENST00000684511.1(ENSG00000288714):​n.35+80982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0903 in 151,480 control chromosomes in the GnomAD database, including 1,248 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 0.090 (1248 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000684511.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

ENSG00000288714 (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 (AFR) allele frequency at 95% confidence interval = 0.229 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
ENSG00000288714	ENST00000684511.1	n.35+80982C>T		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13662 AN: 151362 Hom.: 1248 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0903 AC: 13674 AN: 151480 Hom.: 1248 Cov.: 32 AF XY: 0.0881 AC XY: 6519 AN XY: 74036

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0462

Gnomad4 ASJ AF: 0.0528

Gnomad4 EAS AF: 0.000389

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.0654

Alfa AF: 0.0457 Hom.: 326

Bravo AF: 0.0986

Asia WGS AF: 0.0310 AC: 110 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	0.90
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17069951; hg19: chr6-140717053;