rs9607469

Variant names:

• chr22-37523260-G-A
• rs9607469
• ENST00000812356.1:n.564-96C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-37523260-G-A
• chr22-37523260-G-C

Variant summary

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

The ENST00000812356.1(ENSG00000305681):​n.564-96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,654 control chromosomes in the GnomAD database, including 2,202 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 0.17 (2202 hom., cov: 30)
• Consequence: ENSG00000305681 ENST00000812356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 25 publications found

Genes affected

ENSG00000305681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305681	ENST00000812356.1	n.564-96C>T		intron_variant	Intron 2 of 2
ENSG00000305681	ENST00000812357.1	n.537-91C>T		intron_variant	Intron 2 of 2
ENSG00000305681	ENST00000812358.1	n.645-91C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25684 AN: 151536 Hom.: 2207 Cov.: 30

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.169 AC: 25669 AN: 151654 Hom.: 2202 Cov.: 30 AF XY: 0.169 AC XY: 12553 AN XY: 74098

African (AFR) AF: 0.162 AC: 6678 AN: 41312

American (AMR) AF: 0.135 AC: 2061 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1036 AN: 5110

South Asian (SAS) AF: 0.243 AC: 1166 AN: 4802

European-Finnish (FIN) AF: 0.173 AC: 1827 AN: 10534

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11686 AN: 67860

Other (OTH) AF: 0.181 AC: 382 AN: 2112

Alfa AF: 0.168 Hom.: 7324

Bravo AF: 0.163

Asia WGS AF: 0.205 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs9607469; hg19: chr22-37919267;