rs9909416

Variant names:

• chr17-35870979-C-T
• rs9909416
• ENST00000605548.2:n.183+1861C>T

Variant summary

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

The ENST00000605548.2(ENSG00000270240):​n.183+1861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,056 control chromosomes in the GnomAD database, including 2,139 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 0.16 (2139 hom., cov: 31)
• Consequence: ENSG00000270240 ENST00000605548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744
• Publications: 6 publications found

Genes affected

ENSG00000270240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371745	XR_007065724.1	n.147+1861C>T		intron_variant	Intron 1 of 4
LOC105371745	XR_934699.2	n.147+1861C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270240	ENST00000605548.2	n.183+1861C>T		intron_variant	Intron 1 of 4	3
ENSG00000270240	ENST00000788503.1	n.184+1861C>T		intron_variant	Intron 1 of 4
ENSG00000270240	ENST00000788504.1	n.155+1861C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24059 AN: 151938 Hom.: 2127 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.158 AC: 24100 AN: 152056 Hom.: 2139 Cov.: 31 AF XY: 0.159 AC XY: 11852 AN XY: 74336

African (AFR) AF: 0.189 AC: 7843 AN: 41452

American (AMR) AF: 0.179 AC: 2730 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1711 AN: 5172

South Asian (SAS) AF: 0.128 AC: 618 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1554 AN: 10570

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8565 AN: 67994

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.135 Hom.: 212

Bravo AF: 0.167

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.29
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs9909416; hg19: chr17-34197983;