rs9294466

Variant names:

• chr6-90801676-A-T
• rs9294466
• XR_001744259.1:n.1244-106380A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744259.1(LOC107986623):​n.1244-106380A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 1 publications found

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-106380A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.257 AC: 10653 AN: 41490

American (AMR) AF: 0.227 AC: 3464 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5160

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1133 AN: 10602

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9491 AN: 67974

Other (OTH) AF: 0.192 AC: 406 AN: 2112

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs9294466; hg19: chr6-91511394;