rs17032647

Variant names:

• chr2-106206308-C-T
• rs17032647
• ENST00000771335.1:n.143+6686C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000771335.1(ENSG00000300396):​n.143+6686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 152,250 control chromosomes in the GnomAD database, including 35 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 0.015 (35 hom., cov: 30)
• Consequence: ENSG00000300396 ENST00000771335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 0 publications found

Genes affected

ENSG00000300396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0149 (2266/152250) while in subpopulation AMR AF = 0.0483 (738/15294). AF 95% confidence interval is 0.0454. There are 35 homozygotes in GnomAd4. There are 1089 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 35 gene

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
ENSG00000300396	ENST00000771335.1	n.143+6686C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0148 AC: 2259 AN: 152132 Hom.: 31 Cov.: 30

Gnomad AFR AF: 0.00372

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.00810

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0149 AC: 2266 AN: 152250 Hom.: 35 Cov.: 30 AF XY: 0.0146 AC XY: 1089 AN XY: 74440

African (AFR) AF: 0.00371 AC: 154 AN: 41538

American (AMR) AF: 0.0483 AC: 738 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.00831 AC: 43 AN: 5176

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4818

European-Finnish (FIN) AF: 0.00810 AC: 86 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0160 AC: 1088 AN: 68020

Other (OTH) AF: 0.0156 AC: 33 AN: 2114

Alfa AF: 0.0181 Hom.: 74

Bravo AF: 0.0191

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.45
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs17032647; hg19: chr2-106822764;