rs7022183

Variant names:

• chr9-13016818-T-C
• rs7022183
• ENST00000649120.1:n.326-11514A>G

Variant summary

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

The ENST00000649120.1(ENSG00000285637):​n.326-11514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,042 control chromosomes in the GnomAD database, including 6,277 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 0.21 (6277 hom., cov: 32)
• Consequence: ENSG00000285637 ENST00000649120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

Genes affected

ENSG00000285637 (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 (AFR) allele frequency at 95% confidence interval = 0.507 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
ENSG00000285637	ENST00000649120.1	n.326-11514A>G		intron_variant	Intron 2 of 5
ENSG00000285637	ENST00000666564.1	n.326-11514A>G		intron_variant	Intron 2 of 4
ENSG00000285637	ENST00000826321.1	n.713-11514A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32382 AN: 151924 Hom.: 6255 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.213 AC: 32458 AN: 152042 Hom.: 6277 Cov.: 32 AF XY: 0.213 AC XY: 15822 AN XY: 74356

African (AFR) AF: 0.512 AC: 21226 AN: 41434

American (AMR) AF: 0.191 AC: 2915 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3466

East Asian (EAS) AF: 0.134 AC: 693 AN: 5174

South Asian (SAS) AF: 0.272 AC: 1306 AN: 4810

European-Finnish (FIN) AF: 0.0380 AC: 403 AN: 10618

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5057 AN: 67952

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.120 Hom.: 1139

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7022183; hg19: chr9-13016817;