rs17162082

Variant names:

• chr1-143545399-C-T
• rs17162082
• ENST00000449715.1:n.666+221C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449715.1(ENSG00000203825):​n.666+221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 148,078 control chromosomes in the GnomAD database, including 879 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 0.047 (879 hom., cov: 31)
• Consequence: ENSG00000203825 ENST00000449715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

Genes affected

ENSG00000203825 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

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
ENSG00000203825	ENST00000449715.1	n.666+221C>T		intron_variant	Intron 4 of 16	6

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 6919 AN: 147966 Hom.: 877 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00111

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0131

Gnomad NFE AF: 0.000408

Gnomad OTH AF: 0.0375

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

GnomAD4 genome AF: 0.0468 AC: 6932 AN: 148078 Hom.: 879 Cov.: 31 AF XY: 0.0451 AC XY: 3254 AN XY: 72190

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0168

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000886

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000408

Gnomad4 OTH AF: 0.0371

Alfa AF: 0.0193 Hom.: 99

Asia WGS AF: 0.00592 AC: 20 AN: 3392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17162082; hg19: chr1-149040066;