rs12122100

chr1-147037378-T-C

Variant summary

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

The NR_024442.2(LOC728989):n.90+5572A>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 0.765 in 152,030 control chromosomes in the GnomAD database, including 44,860 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 0.77 (44860 hom., cov: 32)
• Consequence: LOC728989 NR_024442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC728989	NR_024442.2	n.90+5572A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000444082.2	n.988+4018A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116200 AN: 151912 Hom.: 44797 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.765 AC: 116326 AN: 152030 Hom.: 44860 Cov.: 32 AF XY: 0.775 AC XY: 57563 AN XY: 74318

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.772

Alfa AF: 0.747 Hom.: 45617

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12122100; hg19: chr1-146508934;