rs7022486

Variant names:

• chr9-75409523-C-T
• rs7022486
• ENST00000778465.1:n.109+18240C>T

Variant summary

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

The ENST00000778465.1(ENSG00000301354):​n.109+18240C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 152,220 control chromosomes in the GnomAD database, including 237 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 0.039 (237 hom., cov: 32)
• Consequence: ENSG00000301354 ENST00000778465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 3 publications found

Genes affected

ENSG00000301354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0929 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
ENSG00000301354	ENST00000778465.1	n.109+18240C>T		intron_variant	Intron 1 of 1
ENSG00000301354	ENST00000778466.1	n.271+3491C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0391 AC: 5952 AN: 152102 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.00735

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00910

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0394 AC: 5997 AN: 152220 Hom.: 237 Cov.: 32 AF XY: 0.0404 AC XY: 3004 AN XY: 74432

African (AFR) AF: 0.0954 AC: 3961 AN: 41516

American (AMR) AF: 0.0418 AC: 639 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3470

East Asian (EAS) AF: 0.0582 AC: 301 AN: 5172

South Asian (SAS) AF: 0.0550 AC: 265 AN: 4820

European-Finnish (FIN) AF: 0.00735 AC: 78 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00910 AC: 619 AN: 68014

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.0170 Hom.: 78

Bravo AF: 0.0429

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7022486; hg19: chr9-78024439;