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:58767):

LOC105371745 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605548.2. 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
	ENSG00000270240	ENST00000605548.2	TSL:3	n.183+1861C>T		intron	N/A
	ENSG00000270240	ENST00000788503.1		n.184+1861C>T		intron	N/A
	ENSG00000270240	ENST00000788504.1		n.155+1861C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9909416;

hg19: chr17-34197983;