rs12122440

chr1-76011522-A-C

Variant summary

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

The NR_125939.1(LOC101927342):n.75+124A>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 0.146 in 152,114 control chromosomes in the GnomAD database, including 1,857 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 0.15 (1857 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: LOC101927342 NR_125939.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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 (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927342	NR_125939.1	n.75+124A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663316.1	n.610+124A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22233 AN: 152000 Hom.: 1854 Cov.: 31

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.146 AC: 22255 AN: 152114 Hom.: 1857 Cov.: 31 AF XY: 0.146 AC XY: 10889 AN XY: 74362

Gnomad4 AFR AF: 0.0711

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.140

Alfa AF: 0.168 Hom.: 1740

Bravo AF: 0.141

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.11
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12122440; hg19: chr1-76477207;