rs12122453

chr1-147032561-G-C

Variant summary

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

The NR_024442.2(LOC728989):n.91-7637C>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 0.626 in 152,070 control chromosomes in the GnomAD database, including 30,116 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 0.63 (30116 hom., cov: 32)
• Consequence: LOC728989 NR_024442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC728989	NR_024442.2	n.91-7637C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000444082.2	n.989-1423C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95017 AN: 151950 Hom.: 30069 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.626 AC: 95130 AN: 152070 Hom.: 30116 Cov.: 32 AF XY: 0.637 AC XY: 47350 AN XY: 74326

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.624

Alfa AF: 0.616 Hom.: 3562

Bravo AF: 0.626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12122453; hg19: chr1-146504114;