rs9366868

Variant names:

• chr6-11703267-G-A
• rs9366868
• XR_001743973.2:n.163+3004G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-11703267-G-A
• chr6-11703267-G-C
• chr6-11703267-G-T

Variant summary

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

The XR_001743973.2(LOC340184):​n.163+3004G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,188 control chromosomes in the GnomAD database, including 8,240 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 0.31 (8240 hom., cov: 33)
• Consequence: LOC340184 XR_001743973.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

LOC340184 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC340184	XR_001743973.2	n.163+3004G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46954 AN: 152070 Hom.: 8241 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.309 AC: 46953 AN: 152188 Hom.: 8240 Cov.: 33 AF XY: 0.306 AC XY: 22770 AN XY: 74400

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.307

Alfa AF: 0.251 Hom.: 801

Bravo AF: 0.294

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9366868; hg19: chr6-11703500;