chr22-30909855-G-A

Variant names:

• chr22-30909855-G-A
• rs714023
• ENST00000720523.1:n.174+1443C>T

Variant summary

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

The NR_146603.1(LOC107985544):​n.326+1443C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 152,186 control chromosomes in the GnomAD database, including 983 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 0.096 (983 hom., cov: 33)
• Consequence: LOC107985544 NR_146603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 2 publications found

Genes affected

ENSG00000294008 (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 (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146603.1. 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
	LOC107985544	NR_146603.1		n.326+1443C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294008	ENST00000720523.1		n.174+1443C>T		intron	N/A
	ENSG00000294008	ENST00000720524.1		n.802+1443C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14616 AN: 152068 Hom.: 983 Cov.: 33

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0960 AC: 14607 AN: 152186 Hom.: 983 Cov.: 33 AF XY: 0.0953 AC XY: 7087 AN XY: 74390

African (AFR) AF: 0.0244 AC: 1014 AN: 41522

American (AMR) AF: 0.0742 AC: 1134 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.0361 AC: 174 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2047 AN: 10588

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9571 AN: 68000

Other (OTH) AF: 0.0926 AC: 195 AN: 2106

Alfa AF: 0.121 Hom.: 1371

Bravo AF: 0.0857

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs714023; hg19: chr22-31305842;