rs11135876

chr8-25619866-C-T

Variant summary

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

The ENST00000670669.1(ENSG00000253100):n.131-10309C>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 0.269 in 151,910 control chromosomes in the GnomAD database, including 6,855 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 0.27 (6855 hom., cov: 33)
• Consequence: ENST00000670669.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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
	ENST00000670669.1	n.131-10309C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40762 AN: 151792 Hom.: 6831 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.269 AC: 40845 AN: 151910 Hom.: 6855 Cov.: 33 AF XY: 0.270 AC XY: 20025 AN XY: 74250

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.223

Alfa AF: 0.176 Hom.: 2664

Bravo AF: 0.273

Asia WGS AF: 0.300 AC: 1044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.3
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11135876; hg19: chr8-25477382;