rs12237914

Positions:

• chr9-6306896-A-G
• chr9-6306896-A-T

Variant summary

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

The XR_001746614.2(LOC107987046):​n.69-15855T>C 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 0.342 in 152,044 control chromosomes in the GnomAD database, including 9,739 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 0.34 (9739 hom., cov: 32)
• Consequence: LOC107987046 XR_001746614.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

Genes affected

LOC107987046 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987046	XR_001746614.2	n.69-15855T>C		intron_variant, non_coding_transcript_variant
LOC107987046	XR_001746613.3	n.69-15855T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51961 AN: 151926 Hom.: 9721 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.342 AC: 51972 AN: 152044 Hom.: 9739 Cov.: 32 AF XY: 0.341 AC XY: 25327 AN XY: 74330

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.348

Alfa AF: 0.387 Hom.: 16898

Bravo AF: 0.327

Asia WGS AF: 0.514 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12237914; hg19: chr9-6306896;