rs11651398

chr17-78326473-C-T

Variant summary

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

The ENST00000586321.1(ENSG00000267737):n.60+10685C>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 0.0701 in 152,200 control chromosomes in the GnomAD database, including 477 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 0.070 (477 hom., cov: 31)
• Consequence: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.098 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
	ENST00000586321.1	n.60+10685C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10672 AN: 152082 Hom.: 476 Cov.: 31

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0701

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

GnomAD4 genome AF: 0.0701 AC: 10671 AN: 152200 Hom.: 477 Cov.: 31 AF XY: 0.0683 AC XY: 5084 AN XY: 74418

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.0517

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0597

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0693

Alfa AF: 0.0891 Hom.: 369

Bravo AF: 0.0652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.95
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11651398; hg19: chr17-76322554;