chr1-76011522-A-C

Variant names:

• chr1-76011522-A-C
• rs12122440
• ENST00000436121.3:n.396+124A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125939.1(LOC101927342):​n.75+124A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 7 publications found

Genes affected

ENSG00000225605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125939.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927342	NR_125939.1		n.75+124A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225605	ENST00000436121.3	TSL:5	n.396+124A>C		intron	N/A
	ENSG00000225605	ENST00000635455.1	TSL:5	n.675+124A>C		intron	N/A
	ENSG00000225605	ENST00000653726.1		n.551+124A>C		intron	N/A

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

African (AFR) AF: 0.0711 AC: 2952 AN: 41536

American (AMR) AF: 0.177 AC: 2699 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3468

East Asian (EAS) AF: 0.120 AC: 622 AN: 5176

South Asian (SAS) AF: 0.218 AC: 1046 AN: 4794

European-Finnish (FIN) AF: 0.161 AC: 1702 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12205 AN: 67966

Other (OTH) AF: 0.140 AC: 296 AN: 2116

Alfa AF: 0.160 Hom.: 2044

Bravo AF: 0.141

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12122440; hg19: chr1-76477207;