rs320209

Variant names:

• chr9-102182473-A-T
• rs320209
• ENST00000737266.1:n.94+13917A>T

Variant summary

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

The ENST00000737266.1(ENSG00000296202):​n.94+13917A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0768 in 152,154 control chromosomes in the GnomAD database, including 603 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 0.077 (603 hom., cov: 32)
• Consequence: ENSG00000296202 ENST00000737266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 5 publications found

Genes affected

ENSG00000296202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737266.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296202	ENST00000737266.1		n.94+13917A>T		intron	N/A
	ENSG00000296202	ENST00000737267.1		n.94+13917A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11676 AN: 152036 Hom.: 601 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0589

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0768 AC: 11680 AN: 152154 Hom.: 603 Cov.: 32 AF XY: 0.0759 AC XY: 5646 AN XY: 74360

African (AFR) AF: 0.0189 AC: 784 AN: 41560

American (AMR) AF: 0.0869 AC: 1327 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3470

East Asian (EAS) AF: 0.149 AC: 767 AN: 5154

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4818

European-Finnish (FIN) AF: 0.110 AC: 1162 AN: 10570

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6857 AN: 67990

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0962 Hom.: 370

Bravo AF: 0.0749

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs320209; hg19: chr9-104944755;