rs9294466

chr6-90801676-A-T

Variant summary

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

The XR_001744259.1(LOC107986623):n.1244-106380A>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 0.183 in 152,094 control chromosomes in the GnomAD database, including 2,852 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 0.18 (2852 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

LOC107986623 (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 (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986623	XR_001744259.1	n.1244-106380A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27862 AN: 151976 Hom.: 2841 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.183 AC: 27903 AN: 152094 Hom.: 2852 Cov.: 32 AF XY: 0.182 AC XY: 13537 AN XY: 74338

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.0714

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.192

Alfa AF: 0.164 Hom.: 273

Bravo AF: 0.196

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9294466; hg19: chr6-91511394;