rs1422122

Variant names:

• chr5-86077386-A-G
• rs1422122
• ENST00000767533.1:n.135-10435A>G

Variant summary

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

The ENST00000767533.1(ENSG00000299923):​n.135-10435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,006 control chromosomes in the GnomAD database, including 8,093 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 0.32 (8093 hom., cov: 32)
• Consequence: ENSG00000299923 ENST00000767533.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 1 publications found

Genes affected

ENSG00000299923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767533.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299923	ENST00000767533.1		n.135-10435A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48476 AN: 151886 Hom.: 8097 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.319 AC: 48484 AN: 152006 Hom.: 8093 Cov.: 32 AF XY: 0.315 AC XY: 23373 AN XY: 74316

African (AFR) AF: 0.229 AC: 9487 AN: 41492

American (AMR) AF: 0.325 AC: 4951 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1201 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2429 AN: 5156

South Asian (SAS) AF: 0.334 AC: 1610 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3115 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24621 AN: 67940

Other (OTH) AF: 0.323 AC: 680 AN: 2108

Alfa AF: 0.349 Hom.: 5303

Bravo AF: 0.320

Asia WGS AF: 0.403 AC: 1403 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		-0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1422122;

hg19: chr5-85373204;