rs9383242

Positions:

• chr6-17066364-T-A
• chr6-17066364-T-C
• chr6-17066364-T-G

Variant summary

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

The XR_007059481.1(LOC124901269):​n.39-5530A>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 0.823 in 152,102 control chromosomes in the GnomAD database, including 52,695 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 0.82 (52695 hom., cov: 32)
• Consequence: LOC124901269 XR_007059481.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

LOC124901269 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901269	XR_007059481.1	n.39-5530A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125142 AN: 151986 Hom.: 52674 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.823 AC: 125206 AN: 152102 Hom.: 52695 Cov.: 32 AF XY: 0.827 AC XY: 61517 AN XY: 74352

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.852

Alfa AF: 0.856 Hom.: 7022

Bravo AF: 0.808

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9383242; hg19: chr6-17066595;