rs9612574

Variant names:

• chr22-20656929-G-C
• rs9612574
• ENST00000433066.2:n.58C>G

Variant summary

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

The ENST00000433066.2(ENSG00000290981):​n.58C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 152,302 control chromosomes in the GnomAD database, including 599 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 0.085 (598 hom., cov: 31)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: ENSG00000290981 ENST00000433066.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 5 publications found

Genes affected

ENSG00000290981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433066.2. 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
	ENSG00000290981	ENST00000433066.2	TSL:3	n.58C>G		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000290981	ENST00000731909.1		n.5C>G		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000290981	ENST00000731910.1		n.30C>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0853 AC: 12968 AN: 152110 Hom.: 598 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0938

GnomAD4 exome AF: 0.162 AC: 12 AN: 74 Hom.: 1 Cov.: 0 AF XY: 0.115 AC XY: 6 AN XY: 52

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 9 AN: 54

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.0853 AC: 12983 AN: 152228 Hom.: 598 Cov.: 31 AF XY: 0.0839 AC XY: 6244 AN XY: 74426

African (AFR) AF: 0.126 AC: 5242 AN: 41550

American (AMR) AF: 0.0721 AC: 1104 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3470

East Asian (EAS) AF: 0.0483 AC: 248 AN: 5138

South Asian (SAS) AF: 0.0673 AC: 325 AN: 4826

European-Finnish (FIN) AF: 0.0567 AC: 601 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0727 AC: 4942 AN: 68012

Other (OTH) AF: 0.0933 AC: 197 AN: 2112

Alfa AF: 0.0736 Hom.: 45

Bravo AF: 0.0884

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		0.20

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: rs9612574;

hg19: chr22-21011216;