rs9264904

Positions:

• chr6-31304776-G-A

Variant summary

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

The XR_926691.3(LOC112267902):​n.964+2002C>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 0.291 in 151,994 control chromosomes in the GnomAD database, including 6,708 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 0.29 (6708 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.964+2002C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44242 AN: 151876 Hom.: 6702 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.291 AC: 44289 AN: 151994 Hom.: 6708 Cov.: 31 AF XY: 0.288 AC XY: 21430 AN XY: 74304

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.347

Alfa AF: 0.277 Hom.: 6247

Bravo AF: 0.302

Asia WGS AF: 0.254 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9264904; hg19: chr6-31272553; COSMIC: COSV69706116; COSMIC: COSV69706116;