rs12375686

chr9-117654894-T-G

Variant summary

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

The NR_109806.1(LOC101928797):n.488-714T>G 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 0.059 in 152,264 control chromosomes in the GnomAD database, including 333 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 0.059 (333 hom., cov: 32)
• Consequence: LOC101928797 NR_109806.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928797	NR_109806.1	n.488-714T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000450938.1	n.488-714T>G		intron_variant, non_coding_transcript_variant		1
	ENST00000657171.1	n.486-714T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8988 AN: 152146 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0590 AC: 8982 AN: 152264 Hom.: 333 Cov.: 32 AF XY: 0.0607 AC XY: 4518 AN XY: 74454

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.0482

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0683 Hom.: 72

Bravo AF: 0.0507

Asia WGS AF: 0.0680 AC: 235 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	0.62
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12375686; hg19: chr9-120417172;