rs17444745

Variant names:

• chr16-85927956-G-A
• rs17444745
• ENST00000646214.1:n.77+2896G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-85927956-G-A
• chr16-85927956-G-C
• chr16-85927956-G-T

Variant summary

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

The ENST00000646214.1(ENSG00000285163):​n.77+2896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,198 control chromosomes in the GnomAD database, including 1,437 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 0.12 (1437 hom., cov: 32)
• Consequence: ENSG00000285163 ENST00000646214.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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
ENSG00000285163	ENST00000646214.1	n.77+2896G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18333 AN: 152080 Hom.: 1435 Cov.: 32

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.120 AC: 18333 AN: 152198 Hom.: 1437 Cov.: 32 AF XY: 0.119 AC XY: 8844 AN XY: 74420

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0934

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.148

Alfa AF: 0.145 Hom.: 1824

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17444745; hg19: chr16-85961562;