ENST00000816240.1:n.219+12006T>C

Variant names:

• chr9-2256092-T-C
• rs16938145
• ENST00000816240.1:n.219+12006T>C

Variant summary

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

The ENST00000816240.1(ENSG00000306202):​n.219+12006T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,134 control chromosomes in the GnomAD database, including 3,895 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 0.22 (3895 hom., cov: 33)
• Consequence: ENSG00000306202 ENST00000816240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 3 publications found

Genes affected

ENSG00000306202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816240.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306202	ENST00000816240.1		n.219+12006T>C		intron	N/A
	ENSG00000306202	ENST00000816241.1		n.315+12006T>C		intron	N/A
	ENSG00000306202	ENST00000816242.1		n.247-8143T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33523 AN: 152016 Hom.: 3886 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.221 AC: 33556 AN: 152134 Hom.: 3895 Cov.: 33 AF XY: 0.221 AC XY: 16406 AN XY: 74392

African (AFR) AF: 0.291 AC: 12063 AN: 41488

American (AMR) AF: 0.212 AC: 3241 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.0666 AC: 345 AN: 5180

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4816

European-Finnish (FIN) AF: 0.209 AC: 2207 AN: 10582

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13409 AN: 67982

Other (OTH) AF: 0.200 AC: 423 AN: 2114

Alfa AF: 0.194 Hom.: 3192

Bravo AF: 0.220

Asia WGS AF: 0.176 AC: 609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs16938145; hg19: chr9-2256092;