rs11008099

chr10-30545703-G-Achr10-30545703-G-T

Variant summary

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

The ENST00000670247.1(ENSG00000287420):n.327-8251G>A 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 0.0758 in 152,028 control chromosomes in the GnomAD database, including 596 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 0.076 (596 hom., cov: 31)
• Consequence: ENST00000670247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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 (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376478	XR_007062102.1	n.181-8251G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670247.1	n.327-8251G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11519 AN: 151910 Hom.: 594 Cov.: 31

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.0758 AC: 11527 AN: 152028 Hom.: 596 Cov.: 31 AF XY: 0.0750 AC XY: 5575 AN XY: 74322

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.0600

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.0860

Alfa AF: 0.0792 Hom.: 533

Bravo AF: 0.0737

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.47
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: rs11008099; hg19: chr10-30834632;